-/* Generated by Cython 0.13 on Tue Jun 7 17:24:36 2011 */
+/* Generated by Cython 0.16 on Thu Nov 22 15:20:54 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
+#elif PY_VERSION_HEX < 0x02040000
+ #error Cython requires Python 2.4+.
#else
-
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#define PY_LONG_LONG LONG_LONG
#endif
-#if PY_VERSION_HEX < 0x02040000
- #define METH_COEXIST 0
- #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
- #define PyDict_Contains(d,o) PySequence_Contains(d,o)
+#ifndef Py_HUGE_VAL
+ #define Py_HUGE_VAL HUGE_VAL
+#endif
+
+#ifdef PYPY_VERSION
+#define CYTHON_COMPILING_IN_PYPY 1
+#define CYTHON_COMPILING_IN_CPYTHON 0
+#else
+#define CYTHON_COMPILING_IN_PYPY 0
+#define CYTHON_COMPILING_IN_CPYTHON 1
+#endif
+
+#if CYTHON_COMPILING_IN_PYPY
+ #define __Pyx_PyCFunction_Call PyObject_Call
+#else
+ #define __Pyx_PyCFunction_Call PyCFunction_Call
#endif
#if PY_VERSION_HEX < 0x02050000
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) PyInt_AsLong(o)
+ #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
#define PyNumber_Index(o) PyNumber_Int(o)
#define PyIndex_Check(o) PyNumber_Check(o)
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+ #define __PYX_BUILD_PY_SSIZE_T "i"
+#else
+ #define __PYX_BUILD_PY_SSIZE_T "n"
#endif
#if PY_VERSION_HEX < 0x02060000
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#endif
+
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
+
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
+#if PY_VERSION_HEX < 0x03020000
+ typedef long Py_hash_t;
+ #define __Pyx_PyInt_FromHash_t PyInt_FromLong
+ #define __Pyx_PyInt_AsHash_t PyInt_AsLong
+#else
+ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
+ #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
+#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
#if PY_MAJOR_VERSION >= 3
#define __Pyx_DOCSTR(n) (n)
#endif
-#ifdef __cplusplus
-#define __PYX_EXTERN_C extern "C"
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
#else
-#define __PYX_EXTERN_C extern
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
+#ifndef __PYX_EXTERN_C
+ #ifdef __cplusplus
+ #define __PYX_EXTERN_C extern "C"
+ #else
+ #define __PYX_EXTERN_C extern
+ #endif
#endif
#if defined(WIN32) || defined(MS_WINDOWS)
#define _USE_MATH_DEFINES
#endif
#include <math.h>
+#define __PYX_HAVE__csamtools
#define __PYX_HAVE_API__csamtools
#include "string.h"
#include "stdlib.h"
#include "stdio.h"
#include "ctype.h"
#include "unistd.h"
-#include "fileobject.h"
#include "razf.h"
#include "stdint.h"
#include "bam.h"
#include "sam.h"
-#include "glf.h"
-#include "bam_maqcns.h"
#include "faidx.h"
#include "pysam_util.h"
#include "pythread.h"
+#ifdef _OPENMP
+#include <omp.h>
+#endif /* _OPENMP */
+
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
/* inline attribute */
#ifndef CYTHON_INLINE
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
+#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-
+#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
-/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
-#define likely(x) __builtin_expect(!!(x), 1)
-#define unlikely(x) __builtin_expect(!!(x), 0)
-#else /* __GNUC__ > 2 ... */
-#define likely(x) (x)
-#define unlikely(x) (x)
-#endif /* __GNUC__ > 2 ... */
+ /* Test for GCC > 2.95 */
+ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+ #else /* __GNUC__ > 2 ... */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+ #endif /* __GNUC__ > 2 ... */
#else /* __GNUC__ */
-#define likely(x) (x)
-#define unlikely(x) (x)
+ #define likely(x) (x)
+ #define unlikely(x) (x)
#endif /* __GNUC__ */
static PyObject *__pyx_m;
static const char *__pyx_f[] = {
"csamtools.pyx",
- "csamtools.pxd",
"bool.pxd",
+ "complex.pxd",
};
-/* Type declarations */
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":388
- * counter[0] += 1;
+/*--- Type declarations ---*/
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr;
+struct __pyx_obj_9csamtools_IteratorRow;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs;
+struct __pyx_obj_9csamtools_IteratorRowAll;
+struct __pyx_obj_9csamtools_PileupProxy;
+struct __pyx_obj_9csamtools_AlignedRead;
+struct __pyx_obj_9csamtools_Fastafile;
+struct __pyx_obj_9csamtools_IteratorRowSelection;
+struct __pyx_obj_9csamtools_IteratorColumn;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs;
+struct __pyx_obj_9csamtools_IteratorRowRegion;
+struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_9csamtools_Samfile;
+struct __pyx_obj_9csamtools_SNPCall;
+struct __pyx_obj_9csamtools_IndexedReads;
+struct __pyx_obj_9csamtools_IteratorColumnRegion;
+struct __pyx_obj_9csamtools_PileupRead;
+struct __pyx_t_9csamtools___iterdata;
+typedef struct __pyx_t_9csamtools___iterdata __pyx_t_9csamtools___iterdata;
+struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData;
+struct __pyx_t_9csamtools_MateData;
+typedef struct __pyx_t_9csamtools_MateData __pyx_t_9csamtools_MateData;
+
+/* "csamtools.pxd":394
+ * # Utility types
*
- * ctypedef struct MateData: # <<<<<<<<<<<<<<
- * char * name
- * bam1_t * mate
- */
-
-typedef struct {
- char *name;
- bam1_t *mate;
- uint32_t flag;
-} __pyx_t_9csamtools_MateData;
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1478
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
* samfile_t * samfile
* bam_iter_t iter
*/
-
-typedef struct {
+struct __pyx_t_9csamtools___iterdata {
samfile_t *samfile;
bam_iter_t iter;
faidx_t *fastafile;
int tid;
char *seq;
int seq_len;
-} __pyx_t_9csamtools___iterdata;
+};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1655
- * bam_plp_set_mask( self.pileup_iter, self.mask )
- *
+/* "csamtools.pxd":523
+ * cdef char * getSequence( self )
+ * cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
* int tid,
* int start,
*/
-
struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData {
int __pyx_n;
int reopen;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3192
- * bam_maqindel_ret_destroy(self._r)
- *
- * cdef class IndelCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
+/* "csamtools.pyx":518
+ * counter[0] += 1;
*
+ * ctypedef struct MateData: # <<<<<<<<<<<<<<
+ * char * name
+ * bam1_t * mate
*/
-
-struct __pyx_obj_9csamtools_IndelCallerBase {
- PyObject_HEAD
- bam_maqindel_opt_t *options;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
- int cap_mapQ;
- int max_depth;
+struct __pyx_t_9csamtools_MateData {
+ char *name;
+ bam1_t *mate;
+ uint32_t flag;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3330
- * return self._call()
- *
- * cdef class IteratorIndelCalls( IndelCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
- *
+/* "csamtools.pyx":140
+ * cdef char* CODE2CIGAR= "MIDNSHP=X"
+ * if IS_PYTHON3:
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-
-struct __pyx_obj_9csamtools_IteratorIndelCalls {
- struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
+ PyObject_HEAD
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
+
+/* "csamtools.pxd":464
+ * cdef uint32_t _is_tail
+ *
+ * cdef class IteratorRow: # <<<<<<<<<<<<<<
+ * pass
*
*/
-
-struct __pyx_obj_9csamtools_Fastafile {
+struct __pyx_obj_9csamtools_IteratorRow {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
- char *_filename;
- faidx_t *fastafile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3103
- * return call
+
+/* "csamtools.pxd":487
+ * cdef int cnext(self)
*
- * cdef class IndelCall: # <<<<<<<<<<<<<<
- * '''the results of an indel call.'''
- * cdef int _tid
+ * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef int tid
*/
-
-struct __pyx_obj_9csamtools_IndelCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- int _coverage;
- int _rms_mapping_quality;
- bam_maqindel_ret_t *_r;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ int tid;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
};
-/* "pysam/csamtools.pxd":388
- * cdef bam1_t * _delegate
+
+/* "csamtools.pxd":480
+ * cdef int cnext(self)
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
*/
-
-struct __pyx_obj_9csamtools_Samfile {
- PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isremote;
+struct __pyx_obj_9csamtools_IteratorRowAll {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
bam1_t *b;
- char *mode;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3287
- * return call
- *
- * cdef class IndelCaller( IndelCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
- *
- */
-
-struct __pyx_obj_9csamtools_IndelCaller {
- struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
-};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":91
- * return dest
+/* "csamtools.pxd":449
+ * cdef char * _getrname( self, int tid )
*
- * cdef class PileupRead # <<<<<<<<<<<<<<
- * cdef makePileupRead( bam_pileup1_t * src ):
- * '''fill a PileupRead object from a bam_pileup1_t * object.'''
+ * cdef class PileupProxy: # <<<<<<<<<<<<<<
+ * cdef bam_pileup1_t ** plp
+ * cdef int tid
*/
-
-struct __pyx_obj_9csamtools_PileupRead {
+struct __pyx_obj_9csamtools_PileupProxy {
PyObject_HEAD
- struct __pyx_obj_9csamtools_AlignedRead *_alignment;
- int32_t _qpos;
- int _indel;
- int _level;
- uint32_t _is_del;
- uint32_t _is_head;
- uint32_t _is_tail;
+ bam_pileup1_t **plp;
+ int tid;
+ int pos;
+ int n_pu;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2816
- * return retval, out_stderr, out_stdout
- *
- * cdef class SNPCall: # <<<<<<<<<<<<<<
- * '''the results of a SNP call.'''
- * cdef int _tid
- */
-
-struct __pyx_obj_9csamtools_SNPCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- char _reference_base;
- char _genotype;
- int _consensus_quality;
- int _snp_quality;
- int _rms_mapping_quality;
- int _coverage;
-};
-/* "pysam/csamtools.pxd":383
+/* "csamtools.pxd":415
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length )
*
- * # need to declare all C fields and methods here
* cdef class AlignedRead: # <<<<<<<<<<<<<<
*
* # object that this AlignedRead represents
*/
-
struct __pyx_obj_9csamtools_AlignedRead {
PyObject_HEAD
bam1_t *_delegate;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542
- * return ret
+
+/* "csamtools.pxd":408
+ * # Note: need to declare all C fields and methods here
+ * #
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to fastafile
+ */
+struct __pyx_obj_9csamtools_Fastafile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
+ char *_filename;
+ faidx_t *fastafile;
+};
+
+
+/* "csamtools.pxd":492
+ * cdef IteratorRowRegion rowiter
+ *
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef int current_pos
+ */
+struct __pyx_obj_9csamtools_IteratorRowSelection {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab;
+ bam1_t *b;
+ int current_pos;
+ samfile_t *fp;
+ PyObject *positions;
+ int owns_samfile;
+};
+
+
+/* "csamtools.pxd":504
+ * cdef int cnext(self)
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over columns.
*
+ * # result of the last plbuf_push
*/
-
struct __pyx_obj_9csamtools_IteratorColumn {
PyObject_HEAD
struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
struct __pyx_obj_9csamtools_Samfile *samfile;
struct __pyx_obj_9csamtools_Fastafile *fastafile;
PyObject *stepper;
+ int max_depth;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712
- * self.iterdata.seq = NULL
- *
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
- */
-
-struct __pyx_obj_9csamtools_IteratorColumnRegion {
- struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
-};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1187
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over mapped reads.
+/* "csamtools.pxd":536
+ * cdef int truncate
*
- */
-
-struct __pyx_obj_9csamtools_IteratorRow {
- PyObject_HEAD
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1356
- * if self.owns_samfile: samclose( self.fp )
+ * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
- * """iterates over all mapped reads by chaining iterators over each reference
- * """
*/
-
-struct __pyx_obj_9csamtools_IteratorRowAllRefs {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_obj_9csamtools_Samfile *samfile;
- int tid;
- struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206
+
+/* "csamtools.pxd":467
* pass
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
- *
+ * cdef bam_iter_t iter # iterator state object
+ * cdef bam1_t * b
*/
-
struct __pyx_obj_9csamtools_IteratorRowRegion {
struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
- * self.n_plp )
+
+/* "csamtools.pyx":142
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
*
- * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
- * """iterates over all columns by chaining iterators over each reference
- * """
*/
-
-struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
- struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr {
+ PyObject_HEAD
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
- * raise StopIteration
- *
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile)*
+
+/* "csamtools.pxd":420
+ * cdef bam1_t * _delegate
*
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
*/
-
-struct __pyx_obj_9csamtools_IteratorRowSelection {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab;
- bam1_t *b;
- int current_pos;
- samfile_t *fp;
- PyObject *positions;
- int owns_samfile;
-};
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873
- *
- *
- * cdef class SNPCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
- *
- */
-
-struct __pyx_obj_9csamtools_SNPCallerBase {
+struct __pyx_obj_9csamtools_Samfile {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtab;
- bam_maqcns_t *c;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
+ struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
+ char *_filename;
+ samfile_t *samfile;
+ bam_index_t *index;
+ int isbam;
+ int isstream;
+ int isremote;
+ bam1_t *b;
+ char *mode;
+ int64_t start_offset;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021
- * return call
- *
- * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
- *
- */
-
-struct __pyx_obj_9csamtools_SNPCaller {
- struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
-};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946
- * sys.stdout.flush()
- *
- * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
+/* "csamtools.pyx":3222
+ * return retval, out_stderr, out_stdout
*
+ * cdef class SNPCall: # <<<<<<<<<<<<<<
+ * '''the results of a SNP call.'''
+ * cdef int _tid
*/
-
-struct __pyx_obj_9csamtools_IteratorSNPCalls {
- struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
+struct __pyx_obj_9csamtools_SNPCall {
+ PyObject_HEAD
+ int _tid;
+ int _pos;
+ char _reference_base;
+ char _genotype;
+ int _consensus_quality;
+ int _snp_quality;
+ int _rms_mapping_quality;
+ int _coverage;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
- *
- */
-
-struct __pyx_obj_9csamtools_IteratorRowAll {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
- bam1_t *b;
- samfile_t *fp;
- int owns_samfile;
-};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3370
- *
+/* "csamtools.pxd":539
+ * pass
*
* cdef class IndexedReads: # <<<<<<<<<<<<<<
- * """index a bamfile by read.
- *
+ * cdef Samfile samfile
+ * cdef samfile_t * fp
*/
-
struct __pyx_obj_9csamtools_IndexedReads {
PyObject_HEAD
struct __pyx_obj_9csamtools_Samfile *samfile;
int owns_samfile;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":82
- * return dest
+
+/* "csamtools.pxd":531
+ * cdef reset( self, tid, start, end )
*
- * cdef class PileupProxy # <<<<<<<<<<<<<<
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * cdef int start
+ * cdef int end
*/
+struct __pyx_obj_9csamtools_IteratorColumnRegion {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+ int start;
+ int end;
+ int truncate;
+};
-struct __pyx_obj_9csamtools_PileupProxy {
+
+/* "csamtools.pxd":455
+ * cdef int n_pu
+ *
+ * cdef class PileupRead: # <<<<<<<<<<<<<<
+ * cdef AlignedRead _alignment
+ * cdef int32_t _qpos
+ */
+struct __pyx_obj_9csamtools_PileupRead {
PyObject_HEAD
- bam_pileup1_t *plp;
- int tid;
- int pos;
- int n_pu;
+ struct __pyx_obj_9csamtools_AlignedRead *_alignment;
+ int32_t _qpos;
+ int _indel;
+ int _level;
+ uint32_t _is_del;
+ uint32_t _is_head;
+ uint32_t _is_tail;
};
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542
+
+/* "csamtools.pyx":1766
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712
+/* "csamtools.pyx":1931
* self.iterdata.seq = NULL
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873
- *
- *
- * cdef class SNPCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_SNPCallerBase {
- PyObject *(*__dump)(struct __pyx_obj_9csamtools_SNPCallerBase *, glf1_t *, uint32_t, int);
-};
-static struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtabptr_9csamtools_SNPCallerBase;
-
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021
- * return call
+/* "csamtools.pyx":1461
*
- * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_SNPCaller {
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_base;
-};
-static struct __pyx_vtabstruct_9csamtools_SNPCaller *__pyx_vtabptr_9csamtools_SNPCaller;
-
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206
- * pass
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
* """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
+/* "csamtools.pyx":1641
* raise StopIteration
*
* cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
+/* "csamtools.pyx":1968
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":415
+/* "csamtools.pyx":545
*
*
* cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
- *
+ * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
+ * add_sq_text = False, check_header = True, check_sq = True )*
*/
struct __pyx_vtabstruct_9csamtools_Samfile {
static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244
+/* "csamtools.pyx":375
* ## Public methods
* ######################################################################
* cdef class Fastafile: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292
+/* "csamtools.pyx":1540
* if self.owns_samfile: samclose( self.fp )
*
* cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *);
};
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
-
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946
- * sys.stdout.flush()
- *
- * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls {
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_base;
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls *__pyx_vtabptr_9csamtools_IteratorSNPCalls;
-
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
-
#if CYTHON_REFNANNY
typedef struct {
void (*INCREF)(void*, PyObject*, int);
void (*FinishContext)(void**);
} __Pyx_RefNannyAPIStruct;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
- static __Pyx_RefNannyAPIStruct * __Pyx_RefNannyImportAPI(const char *modname) {
- PyObject *m = NULL, *p = NULL;
- void *r = NULL;
- m = PyImport_ImportModule((char *)modname);
- if (!m) goto end;
- p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
- if (!p) goto end;
- r = PyLong_AsVoidPtr(p);
- end:
- Py_XDECREF(p);
- Py_XDECREF(m);
- return (__Pyx_RefNannyAPIStruct *)r;
- }
- #define __Pyx_RefNannySetupContext(name) void *__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
- #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
- #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
- #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
- #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
+ #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
+#ifdef WITH_THREAD
+ #define __Pyx_RefNannySetupContext(name, acquire_gil) \
+ if (acquire_gil) { \
+ PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
+ PyGILState_Release(__pyx_gilstate_save); \
+ } else { \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
+ }
+#else
+ #define __Pyx_RefNannySetupContext(name, acquire_gil) \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+#endif
+ #define __Pyx_RefNannyFinishContext() \
+ __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+ #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
- #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r);} } while(0)
+ #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0)
+ #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0)
+ #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
+ #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
- #define __Pyx_RefNannySetupContext(name)
+ #define __Pyx_RefNannyDeclarations
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)
#define __Pyx_RefNannyFinishContext()
#define __Pyx_INCREF(r) Py_INCREF(r)
#define __Pyx_DECREF(r) Py_DECREF(r)
#define __Pyx_GOTREF(r)
#define __Pyx_GIVEREF(r)
+ #define __Pyx_XINCREF(r) Py_XINCREF(r)
#define __Pyx_XDECREF(r) Py_XDECREF(r)
+ #define __Pyx_XGOTREF(r)
+ #define __Pyx_XGIVEREF(r)
#endif /* CYTHON_REFNANNY */
-#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0)
-#define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r);} } while(0)
+#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
+#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#ifndef CYTHON_PROFILE
#define CYTHON_PROFILE 1
#endif
-
#ifndef CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_PROFILE_REUSE_FRAME 0
#endif
-
#if CYTHON_PROFILE
-
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-
#if CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_FRAME_MODIFIER static
#define CYTHON_FRAME_DEL
#define CYTHON_FRAME_MODIFIER
#define CYTHON_FRAME_DEL Py_DECREF(__pyx_frame)
#endif
-
#define __Pyx_TraceDeclarations \
static PyCodeObject *__pyx_frame_code = NULL; \
CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
- int __Pyx_use_tracing = 0;
-
+ int __Pyx_use_tracing = 0;
#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \
__Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \
}
-
#define __Pyx_TraceException() \
if (unlikely(__Pyx_use_tracing( && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyObject *exc_info = __Pyx_GetExceptionTuple(); \
Py_DECREF(exc_info); \
} \
}
-
#define __Pyx_TraceReturn(result) \
if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyThreadState_GET()->c_profilefunc( \
PyThreadState_GET()->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
CYTHON_FRAME_DEL; \
}
-
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/
-
#else
-
#define __Pyx_TraceDeclarations
- #define __Pyx_TraceCall(funcname, srcfile, firstlineno)
- #define __Pyx_TraceException()
- #define __Pyx_TraceReturn(result)
-
+ #define __Pyx_TraceCall(funcname, srcfile, firstlineno)
+ #define __Pyx_TraceException()
+ #define __Pyx_TraceReturn(result)
#endif /* CYTHON_PROFILE */
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
+
+#include <string.h>
+
static CYTHON_INLINE PyObject* __Pyx_tp_new(PyObject* type_obj) {
return (PyObject*) (((PyTypeObject*)(type_obj))->tp_new(
(PyTypeObject*)(type_obj), __pyx_empty_tuple, NULL));
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
-static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
-static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
- const char* function_name, int kw_allowed); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name, PyObject* kw_name); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
Py_DECREF(j);
return r;
}
-
-
#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
if (likely(o != Py_None)) {
if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
-
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
if (likely(o != Py_None)) {
if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
-
-
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
- PyObject *r;
- if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- }
- else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
}
- else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
- r = PySequence_GetItem(o, i);
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
}
- else {
- r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ else if (likely(i >= 0)) {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ return m->sq_item(o, i);
+ }
}
- return r;
-}
-
-static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; }
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
- return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
if (PyList_Append(L, x) < 0) return NULL;
}
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
+
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
+}
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
+ return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+}
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
Py_INCREF(value);
#else
if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) {
- /* these presumably have safe hash functions */
value = PyDict_GetItem(d, key);
if (unlikely(!value)) {
value = default_value;
m = __Pyx_GetAttrString(d, "get");
if (!m) return NULL;
value = PyObject_CallFunctionObjArgs(m, key,
- (default_value == Py_None) ? NULL : default_value, NULL);
+ (default_value == Py_None) ? NULL : default_value, NULL);
Py_DECREF(m);
}
#endif
static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
+
#define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_DelItemInt_Fast(o, i) : \
__Pyx_DelItem_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
int r;
if (!j) return -1;
Py_DECREF(j);
return r;
}
-
static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i) {
- if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && likely(i >= 0))
- return PySequence_DelItem(o, i);
- else {
- PyObject *j = PyInt_FromSsize_t(i);
- return __Pyx_DelItem_Generic(o, j);
+ if (likely(i >= 0)) {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_ass_item)) {
+ return m->sq_ass_item(o, i, (PyObject *)NULL);
+ }
}
+ return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
+
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname); /*proto*/
+
+#define __Pyx_CyFunction_USED 1
+#include <structmember.h>
+#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
+#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
+#define __Pyx_CYFUNCTION_CCLASS 0x04
+#define __Pyx_CyFunction_GetClosure(f) \
+ (((__pyx_CyFunctionObject *) (f))->func_closure)
+#define __Pyx_CyFunction_GetClassObj(f) \
+ (((__pyx_CyFunctionObject *) (f))->func_classobj)
+#define __Pyx_CyFunction_Defaults(type, f) \
+ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
+#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
+ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
+typedef struct {
+ PyCFunctionObject func;
+ int flags;
+ PyObject *func_dict;
+ PyObject *func_weakreflist;
+ PyObject *func_name;
+ PyObject *func_doc;
+ PyObject *func_code;
+ PyObject *func_closure;
+ PyObject *func_classobj; /* No-args super() class cell */
+ void *defaults;
+ int defaults_pyobjects;
+ PyObject *defaults_tuple; /* Const defaults tuple */
+ PyObject *(*defaults_getter)(PyObject *);
+} __pyx_CyFunctionObject;
+static PyTypeObject *__pyx_CyFunctionType = 0;
+#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \
+ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code)
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *,
+ PyMethodDef *ml, int flags,
+ PyObject *self, PyObject *module,
+ PyObject* code);
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
+ size_t size,
+ int pyobjects);
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
+ PyObject *tuple);
+static int __Pyx_CyFunction_init(void);
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
-static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*proto*/
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t);
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t);
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int16_t(int16_t);
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint16_t(uint16_t);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t);
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t);
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
-static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t);
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t);
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
-static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/
-#if PY_MAJOR_VERSION >= 3
-static PyObject* __pyx_print = 0;
-static PyObject* __pyx_print_kwargs = 0;
-#endif
+static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject *);
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/
+static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t);
static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
-static void __Pyx_WriteUnraisable(const char *name); /*proto*/
+static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+#define __Pyx_Generator_USED
+#include <structmember.h>
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+typedef struct {
+ PyObject_HEAD
+ __pyx_generator_body_t body;
+ PyObject *closure;
+ int is_running;
+ int resume_label;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+ PyObject *gi_weakreflist;
+ PyObject *classobj;
+} __pyx_GeneratorObject;
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure);
+static int __pyx_Generator_init(void);
+
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+ int lineno, const char *filename); /*proto*/
+
+static int __Pyx_check_binary_version(void);
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from __builtin__ */
-/* Module declarations from cpython.version */
-/* Module declarations from cpython.ref */
+/* Module declarations from 'cpython.version' */
-/* Module declarations from cpython.exc */
+/* Module declarations from 'cpython.ref' */
-/* Module declarations from cpython.module */
+/* Module declarations from 'cpython.exc' */
-/* Module declarations from cpython.mem */
+/* Module declarations from 'cpython.module' */
-/* Module declarations from cpython.tuple */
+/* Module declarations from 'cpython.mem' */
-/* Module declarations from cpython.list */
+/* Module declarations from 'cpython.tuple' */
-/* Module declarations from libc.stdio */
+/* Module declarations from 'cpython.list' */
-/* Module declarations from cpython.object */
+/* Module declarations from 'libc.stdio' */
-/* Module declarations from cpython.sequence */
+/* Module declarations from 'cpython.object' */
-/* Module declarations from cpython.mapping */
+/* Module declarations from 'cpython.sequence' */
-/* Module declarations from cpython.iterator */
+/* Module declarations from 'cpython.mapping' */
-/* Module declarations from cpython.type */
+/* Module declarations from 'cpython.iterator' */
-/* Module declarations from cpython.number */
+/* Module declarations from 'cpython.type' */
-/* Module declarations from cpython.int */
+/* Module declarations from 'cpython.number' */
-/* Module declarations from __builtin__ */
+/* Module declarations from 'cpython.int' */
-/* Module declarations from cpython.bool */
+/* Module declarations from '__builtin__' */
+/* Module declarations from 'cpython.bool' */
static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;
-/* Module declarations from cpython.long */
-/* Module declarations from cpython.float */
+/* Module declarations from 'cpython.long' */
-/* Module declarations from cpython.complex */
+/* Module declarations from 'cpython.float' */
-/* Module declarations from cpython.string */
+/* Module declarations from '__builtin__' */
-/* Module declarations from cpython.unicode */
+/* Module declarations from 'cpython.complex' */
+static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
-/* Module declarations from cpython.dict */
+/* Module declarations from 'cpython.string' */
-/* Module declarations from cpython.instance */
+/* Module declarations from 'cpython.unicode' */
-/* Module declarations from cpython.function */
+/* Module declarations from 'cpython.dict' */
-/* Module declarations from cpython.method */
+/* Module declarations from 'cpython.instance' */
-/* Module declarations from cpython.weakref */
+/* Module declarations from 'cpython.function' */
-/* Module declarations from cpython.getargs */
+/* Module declarations from 'cpython.method' */
-/* Module declarations from cpython.pythread */
+/* Module declarations from 'cpython.weakref' */
-/* Module declarations from cpython.cobject */
+/* Module declarations from 'cpython.getargs' */
-/* Module declarations from cpython.oldbuffer */
+/* Module declarations from 'cpython.pythread' */
-/* Module declarations from cpython.set */
+/* Module declarations from 'cpython.pystate' */
-/* Module declarations from cpython.buffer */
+/* Module declarations from 'cpython.cobject' */
-/* Module declarations from cpython.bytes */
+/* Module declarations from 'cpython.oldbuffer' */
-/* Module declarations from cpython.pycapsule */
+/* Module declarations from 'cpython.set' */
-/* Module declarations from cpython */
+/* Module declarations from 'cpython.buffer' */
-/* Module declarations from csamtools */
+/* Module declarations from 'cpython.bytes' */
-static PyTypeObject *__pyx_ptype_9csamtools_file = 0;
+/* Module declarations from 'cpython.pycapsule' */
+
+/* Module declarations from 'cpython' */
+
+/* Module declarations from 'csamtools' */
+static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCallerBase = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorSNPCalls = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCaller = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCallerBase = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndelCaller = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorIndelCalls = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0;
+static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0;
+static char *__pyx_v_9csamtools_CODE2CIGAR;
static char *__pyx_v_9csamtools_bam_nt16_rev_table;
static int __pyx_v_9csamtools_max_pos;
+static PyObject *__pyx_f_9csamtools_from_string_and_size(char *, size_t); /*proto*/
+static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools__charptr_to_str(char *); /*proto*/
+static PyObject *__pyx_f_9csamtools__force_str(PyObject *); /*proto*/
static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
-static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *, int, int, int); /*proto*/
+static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
+static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
#define __Pyx_MODULE_NAME "csamtools"
int __pyx_module_is_main_csamtools = 0;
-/* Implementation of csamtools */
-static PyObject *__pyx_builtin_open;
+/* Implementation of 'csamtools' */
static PyObject *__pyx_builtin_object;
+static PyObject *__pyx_builtin_TypeError;
+static PyObject *__pyx_builtin_enumerate;
+static PyObject *__pyx_builtin_ord;
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_OverflowError;
static PyObject *__pyx_builtin_NotImplementedError;
+static PyObject *__pyx_builtin_OSError;
+static PyObject *__pyx_builtin_AttributeError;
+static PyObject *__pyx_builtin_zip;
+static PyObject *__pyx_builtin_sorted;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_StopIteration;
-static PyObject *__pyx_builtin_cmp;
+static PyObject *__pyx_builtin_min;
+static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_chr;
-static PyObject *__pyx_builtin_TypeError;
-static PyObject *__pyx_builtin_range;
-static char __pyx_k_1[] = "\t";
-static char __pyx_k_2[] = "\n";
-static char __pyx_k_3[] = "calling len() on closed file";
-static char __pyx_k_4[] = "could not open file `%s`";
-static char __pyx_k_5[] = "I/O operation on closed file";
-static char __pyx_k_6[] = "no sequence/region supplied.";
-static char __pyx_k_7[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_8[] = "";
-static char __pyx_k_9[] = "start out of range (%i)";
-static char __pyx_k_10[] = "end out of range (%i)";
-static char __pyx_k_11[] = "%s:%i-%i";
-static char __pyx_k_12[] = "invalid file opening mode `%s`";
-static char __pyx_k_13[] = "http:";
-static char __pyx_k_14[] = "ftp:";
-static char __pyx_k_15[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
-static char __pyx_k_16[] = "unequal names and lengths of reference sequences";
-static char __pyx_k_17[] = "-";
-static char __pyx_k_18[] = "file `%s` not found";
-static char __pyx_k_19[] = "could not open file (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_20[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_21[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_22[] = ".bai";
-static char __pyx_k_23[] = "error while opening index `%s` ";
-static char __pyx_k_24[] = "tid %i out of range 0<=tid<%i";
-static char __pyx_k_25[] = "[:-]";
-static char __pyx_k_26[] = "invalid reference `%s`";
-static char __pyx_k_27[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_28[] = "seek only available in bam files";
-static char __pyx_k_30[] = "fetch called on bamfile without index";
-static char __pyx_k_31[] = "callback functionality requires a region/reference";
-static char __pyx_k_32[] = "no index available for fetch";
-static char __pyx_k_33[] = "fetch called for samfile without header";
-static char __pyx_k_34[] = "fetch for a region is not available for sam files";
-static char __pyx_k_35[] = "callback not implemented yet";
-static char __pyx_k_36[] = "read %s: is unpaired";
-static char __pyx_k_37[] = "mate %s: is unmapped";
-static char __pyx_k_38[] = "mate not found";
-static char __pyx_k_40[] = "counting functionality requires a region/reference";
-static char __pyx_k_41[] = "count for a region is not available for sam files";
-static char __pyx_k_42[] = "no index available for pileup";
-static char __pyx_k_43[] = "pileup of samfiles not implemented yet";
-static char __pyx_k_44[] = "@";
-static char __pyx_k_45[] = "header line without '@': '%s'";
-static char __pyx_k_46[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_47[] = ":";
-static char __pyx_k_48[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_49[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_50[] = "@%s";
-static char __pyx_k_51[] = "%s:%s";
-static char __pyx_k_52[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_53[] = "incomplete sequence information in '%s'";
-static char __pyx_k_54[] = "no index available for iteration";
-static char __pyx_k_55[] = "can only use this iterator on bam files";
-static char __pyx_k_56[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_57[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_59[] = "error during iteration";
-static char __pyx_k_60[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_61[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_62[] = "%c";
-static char __pyx_k_63[] = "create_string_buffer";
-static char __pyx_k_64[] = "<cccf";
-static char __pyx_k_65[] = "<cccb";
-static char __pyx_k_66[] = "<ccch";
-static char __pyx_k_67[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_68[] = "<ccci";
-static char __pyx_k_69[] = "<cccB";
-static char __pyx_k_70[] = "<cccH";
-static char __pyx_k_71[] = "<cccI";
-static char __pyx_k_72[] = "<cccc";
-static char __pyx_k_73[] = "<ccc%is";
-static char __pyx_k_74[] = "tags field too large";
-static char __pyx_k_75[] = "tag '%s' not present";
-static char __pyx_k_76[] = "Contig index";
-static char __pyx_k_77[] = "Mapped position on contig";
-static char __pyx_k_78[] = "Contig index for mate pair";
-static char __pyx_k_79[] = "Position of mate pair";
-static char __pyx_k_80[] = "Insert size";
-static char __pyx_k_81[] = "Binary flag";
-static char __pyx_k_82[] = "Count of cigar entries";
-static char __pyx_k_83[] = "Cigar entries";
-static char __pyx_k_84[] = "Mapping quality";
-static char __pyx_k_85[] = "Bam index bin number";
-static char __pyx_k_86[] = "Length of query name";
-static char __pyx_k_87[] = "Query name";
-static char __pyx_k_88[] = "Length of query sequence";
-static char __pyx_k_89[] = "Query sequence";
-static char __pyx_k_90[] = "Quality scores";
-static char __pyx_k_91[] = "Length of auxilary data";
-static char __pyx_k_92[] = "Maximum data length";
-static char __pyx_k_93[] = "Current data length";
-static char __pyx_k_94[] = "%-30s %-10s= %s";
-static char __pyx_k_95[] = "(";
-static char __pyx_k_96[] = ")";
-static char __pyx_k_97[] = "This class cannot be instantiated from Python";
+static PyObject *__pyx_builtin_open;
+static PyObject *__pyx_builtin_UnicodeDecodeError;
+static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile); /* proto */
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other); /* proto */
+static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
+static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */
+static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
+static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */
+static char __pyx_k_1[] = "Argument must be string or unicode.";
+static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
+static char __pyx_k_5[] = "\t";
+static char __pyx_k_6[] = "\n";
+static char __pyx_k_7[] = "calling len() on closed file";
+static char __pyx_k_9[] = "could not open file `%s`";
+static char __pyx_k_10[] = "I/O operation on closed file";
+static char __pyx_k_13[] = "no sequence/region supplied.";
+static char __pyx_k_15[] = "invalid region: start (%i) > end (%i)";
+static char __pyx_k_16[] = "";
+static char __pyx_k_17[] = "start out of range (%i)";
+static char __pyx_k_18[] = "end out of range (%i)";
+static char __pyx_k_19[] = "%s:%i-%i";
+static char __pyx_k_24[] = "invalid file opening mode `%s`";
+static char __pyx_k_26[] = "-";
+static char __pyx_k_27[] = "http:";
+static char __pyx_k_28[] = "ftp:";
+static char __pyx_k_29[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
+static char __pyx_k_30[] = "unequal names and lengths of reference sequences";
+static char __pyx_k_31[] = "@SQ\tSN:%s\tLN:%s\n";
+static char __pyx_k_32[] = "file `%s` not found";
+static char __pyx_k_33[] = "could not open file (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_34[] = "file does not have valid header (mode='%s') - is it BAM format?";
+static char __pyx_k_35[] = "file does not have valid header (mode='%s') - is it SAM format?";
+static char __pyx_k_36[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_37[] = ".bai";
+static char __pyx_k_38[] = "error while opening index `%s` ";
+static char __pyx_k_41[] = "tid %i out of range 0<=tid<%i";
+static char __pyx_k_43[] = "[:-]";
+static char __pyx_k_45[] = "invalid reference `%s`";
+static char __pyx_k_46[] = "invalid coordinates: start (%i) > end (%i)";
+static char __pyx_k_48[] = "seek only available in bam files";
+static char __pyx_k_50[] = "seek no available in streams";
+static char __pyx_k_56[] = "fetch called on bamfile without index";
+static char __pyx_k_58[] = "callback functionality requires a region/reference";
+static char __pyx_k_60[] = "no index available for fetch";
+static char __pyx_k_62[] = "fetching by region is not available for sam files";
+static char __pyx_k_64[] = "callback not implemented yet";
+static char __pyx_k_66[] = "fetch called for samfile without header";
+static char __pyx_k_69[] = "read %s: is unpaired";
+static char __pyx_k_70[] = "mate %s: is unmapped";
+static char __pyx_k_71[] = "mate not found";
+static char __pyx_k_76[] = "counting functionality requires a region/reference";
+static char __pyx_k_79[] = "count for a region is not available for sam files";
+static char __pyx_k_82[] = "no index available for pileup";
+static char __pyx_k_85[] = "pileup of samfiles not implemented yet";
+static char __pyx_k_92[] = "Samfile.mapped only available in bam files";
+static char __pyx_k_95[] = "Samfile.unmapped only available in bam files";
static char __pyx_k__A[] = "A";
+static char __pyx_k__B[] = "B";
static char __pyx_k__C[] = "C";
static char __pyx_k__D[] = "D";
static char __pyx_k__F[] = "F";
+static char __pyx_k__H[] = "H";
static char __pyx_k__I[] = "I";
static char __pyx_k__S[] = "S";
static char __pyx_k__Z[] = "Z";
+static char __pyx_k__a[] = "a";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
static char __pyx_k__f[] = "f";
+static char __pyx_k__h[] = "h";
static char __pyx_k__i[] = "i";
static char __pyx_k__n[] = "n";
static char __pyx_k__r[] = "r";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
-static char __pyx_k__x[] = "x";
-static char __pyx_k_100[] = "No such file or directory: '%s'";
-static char __pyx_k_101[] = "-o";
-static char __pyx_k_102[] = "option -o is forbidden in samtools view";
-static char __pyx_k_103[] = "_rms_mapping_quality";
-static char __pyx_k_104[] = "--> read %i %s %i";
-static char __pyx_k_105[] = "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i";
-static char __pyx_k_106[] = "-------------------------------------\n";
-static char __pyx_k_107[] = "IteratorSNPCalls requires an pileup iterator with reference sequence";
-static char __pyx_k_108[] = "position %i out of bounds on reference sequence (len=%i)";
-static char __pyx_k_109[] = "no reads in region - no call";
-static char __pyx_k_110[] = "%s/%s";
-static char __pyx_k_111[] = "IndelCallerBase requires an pileup iterator with reference sequence";
-static char __pyx_k_112[] = "can only IndexReads on bam files";
-static char __pyx_k_113[] = "read %s not found";
-static char __pyx_k_114[] = "the query name (None if not present)";
-static char __pyx_k_115[] = "the :term:`cigar` alignment (None if not present).\n ";
-static char __pyx_k_116[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_117[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_118[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
-static char __pyx_k_119[] = "aligned query sequence quality values (None if not present)";
-static char __pyx_k_120[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_121[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_122[] = "Length of the aligned query sequence";
-static char __pyx_k_123[] = "the tags in the AUX field.\n\n This property permits convenience access to \n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a \n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n ";
-static char __pyx_k_124[] = "properties flag";
-static char __pyx_k_125[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_126[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_127[] = "0-based leftmost coordinate";
-static char __pyx_k_128[] = "properties bin";
-static char __pyx_k_129[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_130[] = "aligned end position of the read (read only). Returns\n None if not available.";
-static char __pyx_k_131[] = "aligned length of the read (read only). Returns None if\n not available.";
-static char __pyx_k_132[] = "mapping quality";
-static char __pyx_k_133[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_134[] = "the position of the mate";
-static char __pyx_k_135[] = "the insert size";
-static char __pyx_k_136[] = "true if read is paired in sequencing";
-static char __pyx_k_137[] = "true if read is mapped in a proper pair";
-static char __pyx_k_138[] = "true if read itself is unmapped";
-static char __pyx_k_139[] = "true if the mate is unmapped";
-static char __pyx_k_140[] = "true if read is mapped to reverse strand";
-static char __pyx_k_141[] = "true is read is mapped to reverse strand";
-static char __pyx_k_142[] = "true if this is read1";
-static char __pyx_k_143[] = "true if this is read2";
-static char __pyx_k_144[] = "true if not primary alignment";
-static char __pyx_k_145[] = "true if QC failure";
-static char __pyx_k_146[] = "true if optical or PCR duplicate";
-static char __pyx_k_147[] = "a list of reference positions that this read aligns to.";
-static char __pyx_k_148[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_149[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_150[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_151[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n :attr:`pysam.Samfile.references`\n ";
-static char __pyx_k_152[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_153[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
-static char __pyx_k_154[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_155[] = "number of reads mapping to this column.";
-static char __pyx_k_156[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_157[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_158[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_159[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_160[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_161[] = "current sequence length.";
-static char __pyx_k_162[] = "nucleotide position of SNP.";
-static char __pyx_k_163[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_164[] = "the genotype called.";
-static char __pyx_k_165[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_166[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_167[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_168[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_169[] = "sequence of first allele.";
-static char __pyx_k_170[] = "sequence of second allele.";
-static char __pyx_k_171[] = "reads supporting first allele.";
-static char __pyx_k_172[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_173[] = "A pileup column. A pileup column contains \n all the reads that map to a certain target base.\n\n tid \n chromosome ID as is defined in the header \n pos \n the target base coordinate (0-based) \n n \n number of reads mapping to this column \n pileups \n list of reads (:class:`pysam.PileupRead`) aligned to this column \n ";
-static char __pyx_k_174[] = "\n stderr is captured. \n ";
-static char __pyx_k_175[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_176[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
-static char __pyx_k_177[] = "Fastafile._isOpen (line 265)";
-static char __pyx_k_178[] = "Fastafile._open (line 275)";
-static char __pyx_k_179[] = "Fastafile.fetch (line 306)";
-static char __pyx_k_180[] = "Samfile._isOpen (line 464)";
-static char __pyx_k_181[] = "Samfile._hasIndex (line 468)";
-static char __pyx_k_182[] = "Samfile._open (line 472)";
-static char __pyx_k_183[] = "Samfile.gettid (line 612)";
-static char __pyx_k_184[] = "Samfile.getrname (line 621)";
-static char __pyx_k_185[] = "Samfile._parseRegion (line 637)";
-static char __pyx_k_186[] = "Samfile.seek (line 691)";
-static char __pyx_k_187[] = "Samfile.tell (line 702)";
-static char __pyx_k_188[] = "Samfile.fetch (line 713)";
-static char __pyx_k_189[] = "Samfile.mate (line 782)";
-static char __pyx_k_190[] = "Samfile.count (line 825)";
-static char __pyx_k_191[] = "Samfile.pileup (line 869)";
-static char __pyx_k_192[] = "Samfile.close (line 953)";
-static char __pyx_k_193[] = "Samfile.write (line 969)";
-static char __pyx_k_194[] = "Samfile._buildLine (line 1078)";
-static char __pyx_k_195[] = "Samfile.__next__ (line 1173)";
-static char __pyx_k_196[] = "IteratorRowRegion.__next__ (line 1281)";
-static char __pyx_k_197[] = "IteratorRowAll.__next__ (line 1340)";
-static char __pyx_k_198[] = "IteratorRowAllRefs.__next__ (line 1375)";
-static char __pyx_k_199[] = "IteratorRowSelection.__next__ (line 1459)";
-static char __pyx_k_200[] = "IteratorRowSelection";
-static char __pyx_k_201[] = "IteratorColumn.addReference (line 1634)";
-static char __pyx_k_202[] = "IteratorColumn.hasReference (line 1642)";
-static char __pyx_k_203[] = "IteratorColumnRegion.__next__ (line 1724)";
-static char __pyx_k_204[] = "IteratorColumnRegion";
-static char __pyx_k_205[] = "IteratorColumnAllRefs.__next__ (line 1755)";
-static char __pyx_k_206[] = "IteratorColumnAllRefs";
-static char __pyx_k_207[] = "AlignedRead.__str__ (line 1903)";
-static char __pyx_k_208[] = "AlignedRead.compare (line 1928)";
-static char __pyx_k_209[] = "AlignedRead.overlap (line 2512)";
-static char __pyx_k_210[] = "AlignedRead.opt (line 2541)";
-static char __pyx_k_211[] = "AlignedRead.fancy_str (line 2563)";
-static char __pyx_k_212[] = "Outs.setdevice (line 2705)";
-static char __pyx_k_213[] = "Outs.setfile (line 2710)";
-static char __pyx_k_214[] = "Outs.restore (line 2723)";
-static char __pyx_k_215[] = "_samtools_dispatch (line 2734)";
-static char __pyx_k_216[] = "IteratorSNPCalls.__next__ (line 2969)";
-static char __pyx_k_217[] = "SNPCaller.call (line 3041)";
-static char __pyx_k_218[] = "IndelCaller.call (line 3306)";
-static char __pyx_k_219[] = "IteratorIndelCalls.__next__ (line 3353)";
-static char __pyx_k_220[] = "IndexedReads.build (line 3406)";
+static char __pyx_k_100[] = "@";
+static char __pyx_k_102[] = "header line without '@': '%s'";
+static char __pyx_k_104[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_105[] = ":";
+static char __pyx_k_107[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_108[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_109[] = "@%s";
+static char __pyx_k_110[] = "%s:%s";
+static char __pyx_k_111[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_113[] = "incomplete sequence information in '%s'";
+static char __pyx_k_116[] = "can not iterate over samfile without header";
+static char __pyx_k_119[] = "no index available for iteration";
+static char __pyx_k_125[] = "can only use this iterator on bam files";
+static char __pyx_k_126[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_127[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_129[] = "error during iteration";
+static char __pyx_k_132[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_135[] = "%c%i";
+static char __pyx_k_136[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_137[] = "%c";
+static char __pyx_k_138[] = "<";
+static char __pyx_k_140[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_141[] = "2sccI%i%s";
+static char __pyx_k_145[] = "2sc%is";
+static char __pyx_k_147[] = "create_string_buffer";
+static char __pyx_k_148[] = "tag '%s' not present";
+static char __pyx_k_149[] = "unknown auxilliary type '%s'";
+static char __pyx_k_150[] = "Contig index";
+static char __pyx_k_151[] = "Mapped position on contig";
+static char __pyx_k_152[] = "Contig index for mate pair";
+static char __pyx_k_153[] = "Position of mate pair";
+static char __pyx_k_154[] = "Insert size";
+static char __pyx_k_155[] = "Binary flag";
+static char __pyx_k_156[] = "Count of cigar entries";
+static char __pyx_k_157[] = "Cigar entries";
+static char __pyx_k_158[] = "Mapping quality";
+static char __pyx_k_159[] = "Bam index bin number";
+static char __pyx_k_160[] = "Length of query name";
+static char __pyx_k_161[] = "Query name";
+static char __pyx_k_162[] = "Length of query sequence";
+static char __pyx_k_163[] = "Query sequence";
+static char __pyx_k_164[] = "Quality scores";
+static char __pyx_k_165[] = "Length of auxilary data";
+static char __pyx_k_166[] = "Maximum data length";
+static char __pyx_k_167[] = "Current data length";
+static char __pyx_k_168[] = "%-30s %-10s= %s";
+static char __pyx_k_169[] = "(";
+static char __pyx_k_170[] = ")";
+static char __pyx_k_171[] = "This class cannot be instantiated from Python";
+static char __pyx_k_173[] = "PileupProxy accessed after iterator finished";
+static char __pyx_k_177[] = "No such file or directory: '%s'";
+static char __pyx_k_178[] = "-o";
+static char __pyx_k_179[] = "option -o is forbidden in samtools view";
+static char __pyx_k_185[] = "can only IndexReads on bam files";
+static char __pyx_k_186[] = "read %s not found";
+static char __pyx_k_187[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_188[] = "the query name (None if not present)";
+static char __pyx_k_189[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of operations. The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 |\n +-----+--------------+-----+\n |S |BAM_CSOFT_CLIP|4 |\n +-----+--------------+-----+\n |H |BAM_CHARD_CLIP|5 |\n +-----+--------------+-----+\n |P |BAM_CPAD |6 |\n +-----+--------------+-----+\n |= |BAM_CEQUAL |7 |\n +-----+--------------+-----+\n |X |BAM_CDIFF |8 |\n +-----+--------------+-----+\n\n ";
+static char __pyx_k_190[] = "the :term:`cigar` alignment as a string.\n \n Returns the empty string if not present.\n ";
+static char __pyx_k_191[] = "read sequence bases, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.";
+static char __pyx_k_192[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.";
+static char __pyx_k_193[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
+static char __pyx_k_194[] = "aligned query sequence quality values (None if not present). This property is read-only.\n\n In Python 3, this property is of type bytes.";
+static char __pyx_k_195[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_196[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_197[] = "Length of the aligned query sequence";
+static char __pyx_k_198[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n ";
+static char __pyx_k_199[] = "properties flag";
+static char __pyx_k_200[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
+static char __pyx_k_201[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
+static char __pyx_k_202[] = "0-based leftmost coordinate";
+static char __pyx_k_203[] = "properties bin";
+static char __pyx_k_204[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_205[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available.";
+static char __pyx_k_206[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
+static char __pyx_k_207[] = "mapping quality";
+static char __pyx_k_208[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
+static char __pyx_k_209[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_210[] = "the position of the mate\n deprecated, use PNEXT instead.";
+static char __pyx_k_211[] = "the position of the mate";
+static char __pyx_k_212[] = "the insert size\n deprecated: use tlen instead";
+static char __pyx_k_213[] = "the insert size";
+static char __pyx_k_214[] = "true if read is paired in sequencing";
+static char __pyx_k_215[] = "true if read is mapped in a proper pair";
+static char __pyx_k_216[] = "true if read itself is unmapped";
+static char __pyx_k_217[] = "true if the mate is unmapped";
+static char __pyx_k_218[] = "true if read is mapped to reverse strand";
+static char __pyx_k_219[] = "true is read is mapped to reverse strand";
+static char __pyx_k_220[] = "true if this is read1";
+static char __pyx_k_221[] = "true if this is read2";
+static char __pyx_k_222[] = "true if not primary alignment";
+static char __pyx_k_223[] = "true if QC failure";
+static char __pyx_k_224[] = "true if optical or PCR duplicate";
+static char __pyx_k_225[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_226[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
+static char __pyx_k_227[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_228[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_229[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n ";
+static char __pyx_k_230[] = "total number of mapped reads in file.\n ";
+static char __pyx_k_231[] = "total number of unmapped reads in file.\n ";
+static char __pyx_k_232[] = "full contents of the :term:`sam file` header as a string.";
+static char __pyx_k_233[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n ";
+static char __pyx_k_234[] = "the chromosome ID as is defined in the header";
+static char __pyx_k_235[] = "number of reads mapping to this column.";
+static char __pyx_k_236[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
+static char __pyx_k_237[] = "a :class:`pysam.AlignedRead` object of the aligned read";
+static char __pyx_k_238[] = "position of the read base at the pileup site, 0-based";
+static char __pyx_k_239[] = "indel length; 0 for no indel, positive for ins and negative for del";
+static char __pyx_k_240[] = "1 iff the base on the padded read is a deletion";
+static char __pyx_k_241[] = "current sequence length.";
+static char __pyx_k_242[] = "nucleotide position of SNP.";
+static char __pyx_k_243[] = "reference base at pos. ``N`` if no reference sequence supplied.";
+static char __pyx_k_244[] = "the genotype called.";
+static char __pyx_k_245[] = "the genotype quality (Phred-scaled).";
+static char __pyx_k_246[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
+static char __pyx_k_247[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
+static char __pyx_k_248[] = "coverage or read depth - the number of reads involved in the call.";
+static char __pyx_k_249[] = "getfilesystemencoding";
+static char __pyx_k_250[] = "MIDNSHP=X";
+static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)";
+static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN";
+static char __pyx_k_256[] = "/ifs/devel/pysam/pysam/csamtools.pyx";
+static char __pyx_k_257[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
+static char __pyx_k_266[] = "\n stderr is captured.\n ";
+static char __pyx_k_273[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_290[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
static char __pyx_k__CO[] = "CO";
static char __pyx_k__DS[] = "DS";
static char __pyx_k__DT[] = "DT";
+static char __pyx_k__FO[] = "FO";
static char __pyx_k__GO[] = "GO";
static char __pyx_k__HD[] = "HD";
static char __pyx_k__ID[] = "ID";
+static char __pyx_k__KS[] = "KS";
static char __pyx_k__LB[] = "LB";
static char __pyx_k__LN[] = "LN";
static char __pyx_k__M5[] = "M5";
static char __pyx_k__SQ[] = "SQ";
static char __pyx_k__UR[] = "UR";
static char __pyx_k__VN[] = "VN";
-static char __pyx_k___r[] = "_r";
static char __pyx_k__fd[] = "fd";
-static char __pyx_k__fp[] = "fp";
static char __pyx_k__id[] = "id";
static char __pyx_k__os[] = "os";
+static char __pyx_k__rU[] = "rU";
static char __pyx_k__rb[] = "rb";
static char __pyx_k__re[] = "re";
static char __pyx_k__wb[] = "wb";
static char __pyx_k__wh[] = "wh";
static char __pyx_k__all[] = "all";
-static char __pyx_k__bam[] = "bam";
static char __pyx_k__beg[] = "beg";
static char __pyx_k__bin[] = "bin";
static char __pyx_k__chr[] = "chr";
-static char __pyx_k__cmp[] = "cmp";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
+static char __pyx_k__inf[] = "inf";
static char __pyx_k__map[] = "map";
-static char __pyx_k__opt[] = "opt";
-static char __pyx_k__plp[] = "plp";
+static char __pyx_k__max[] = "max";
+static char __pyx_k__min[] = "min";
+static char __pyx_k__ofd[] = "ofd";
+static char __pyx_k__ord[] = "ord";
static char __pyx_k__pos[] = "pos";
-static char __pyx_k__q_r[] = "q_r";
static char __pyx_k__raw[] = "raw";
static char __pyx_k__seq[] = "seq";
static char __pyx_k__sys[] = "sys";
static char __pyx_k__tid[] = "tid";
static char __pyx_k__wbu[] = "wbu";
+static char __pyx_k__zip[] = "zip";
+static char __pyx_k__2scB[] = "2scB";
+static char __pyx_k__2scH[] = "2scH";
+static char __pyx_k__2scI[] = "2scI";
+static char __pyx_k__2scb[] = "2scb";
+static char __pyx_k__2scc[] = "2scc";
+static char __pyx_k__2scf[] = "2scf";
+static char __pyx_k__2sch[] = "2sch";
+static char __pyx_k__2sci[] = "2sci";
static char __pyx_k__Outs[] = "Outs";
-static char __pyx_k___pos[] = "_pos";
-static char __pyx_k___tid[] = "_tid";
static char __pyx_k__args[] = "args";
-static char __pyx_k__call[] = "call";
-static char __pyx_k__cnt1[] = "cnt1";
-static char __pyx_k__cnt2[] = "cnt2";
-static char __pyx_k__core[] = "core";
-static char __pyx_k__data[] = "data";
static char __pyx_k__dup2[] = "dup2";
static char __pyx_k__flag[] = "flag";
-static char __pyx_k__hash[] = "hash";
-static char __pyx_k__iter[] = "iter";
static char __pyx_k__join[] = "join";
static char __pyx_k__mapq[] = "mapq";
static char __pyx_k__mask[] = "mask";
-static char __pyx_k__mate[] = "mate";
static char __pyx_k__mode[] = "mode";
static char __pyx_k__mpos[] = "mpos";
static char __pyx_k__mrnm[] = "mrnm";
static char __pyx_k__mtid[] = "mtid";
-static char __pyx_k__n_pu[] = "n_pu";
-static char __pyx_k__name[] = "name";
static char __pyx_k__open[] = "open";
static char __pyx_k__path[] = "path";
static char __pyx_k__port[] = "port";
static char __pyx_k__qpos[] = "qpos";
static char __pyx_k__qseq[] = "qseq";
static char __pyx_k__qual[] = "qual";
+static char __pyx_k__read[] = "read";
static char __pyx_k__rlen[] = "rlen";
static char __pyx_k__seek[] = "seek";
static char __pyx_k__self[] = "self";
static char __pyx_k__tags[] = "tags";
-static char __pyx_k__tell[] = "tell";
static char __pyx_k__text[] = "text";
static char __pyx_k__view[] = "view";
-static char __pyx_k___call[] = "_call";
+static char __pyx_k__warn[] = "warn";
static char __pyx_k___open[] = "_open";
-static char __pyx_k___qpos[] = "_qpos";
+static char __pyx_k__ascii[] = "ascii";
static char __pyx_k__bqual[] = "bqual";
-static char __pyx_k__build[] = "build";
+static char __pyx_k__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
-static char __pyx_k__cnext[] = "cnext";
-static char __pyx_k__count[] = "count";
-static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__flush[] = "flush";
static char __pyx_k__indel[] = "indel";
static char __pyx_k__index[] = "index";
-static char __pyx_k__isbam[] = "isbam";
static char __pyx_k__isize[] = "isize";
+static char __pyx_k__items[] = "items";
static char __pyx_k__l_aux[] = "l_aux";
static char __pyx_k__level[] = "level";
-static char __pyx_k__n_hap[] = "n_hap";
-static char __pyx_k__n_plp[] = "n_plp";
-static char __pyx_k__q_cns[] = "q_cns";
-static char __pyx_k__q_ref[] = "q_ref";
static char __pyx_k__qname[] = "qname";
-static char __pyx_k__range[] = "range";
-static char __pyx_k__reset[] = "reset";
static char __pyx_k__rname[] = "rname";
static char __pyx_k__setfd[] = "setfd";
static char __pyx_k__split[] = "split";
static char __pyx_k__start[] = "start";
static char __pyx_k__strip[] = "strip";
-static char __pyx_k__theta[] = "theta";
static char __pyx_k__types[] = "types";
static char __pyx_k__where[] = "where";
static char __pyx_k__write[] = "write";
-static char __pyx_k___indel[] = "_indel";
-static char __pyx_k___level[] = "_level";
static char __pyx_k__ctypes[] = "ctypes";
-static char __pyx_k__errmod[] = "errmod";
+static char __pyx_k__decode[] = "decode";
+static char __pyx_k__encode[] = "encode";
static char __pyx_k__exists[] = "exists";
+static char __pyx_k__extend[] = "extend";
static char __pyx_k__fields[] = "fields";
static char __pyx_k__fileno[] = "fileno";
static char __pyx_k__gettid[] = "gettid";
static char __pyx_k__header[] = "header";
-static char __pyx_k__indel1[] = "indel1";
-static char __pyx_k__indel2[] = "indel2";
static char __pyx_k__is_del[] = "is_del";
static char __pyx_k__l_qseq[] = "l_qseq";
-static char __pyx_k__l_text[] = "l_text";
static char __pyx_k__m_data[] = "m_data";
static char __pyx_k__method[] = "method";
static char __pyx_k__object[] = "object";
static char __pyx_k__offset[] = "offset";
-static char __pyx_k__pileup[] = "pileup";
static char __pyx_k__record[] = "record";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__reopen[] = "reopen";
static char __pyx_k__retval[] = "retval";
-static char __pyx_k__rg2lib[] = "rg2lib";
+static char __pyx_k__sorted[] = "sorted";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
static char __pyx_k__struct[] = "struct";
static char __pyx_k__system[] = "system";
static char __pyx_k__IOError[] = "IOError";
-static char __pyx_k__IntType[] = "IntType";
+static char __pyx_k__OSError[] = "OSError";
static char __pyx_k__O_CREAT[] = "O_CREAT";
static char __pyx_k__Samfile[] = "Samfile";
static char __pyx_k__Windows[] = "Windows";
static char __pyx_k____del__[] = "__del__";
static char __pyx_k____str__[] = "__str__";
static char __pyx_k___isOpen[] = "_isOpen";
-static char __pyx_k___is_del[] = "_is_del";
-static char __pyx_k__compare[] = "compare";
-static char __pyx_k__devnull[] = "devnull";
+static char __pyx_k__compile[] = "compile";
+static char __pyx_k__findall[] = "findall";
static char __pyx_k__is_head[] = "is_head";
static char __pyx_k__is_tail[] = "is_tail";
+static char __pyx_k__islower[] = "islower";
static char __pyx_k__isupper[] = "isupper";
static char __pyx_k__l_qname[] = "l_qname";
+static char __pyx_k__lengths[] = "lengths";
static char __pyx_k__mkstemp[] = "mkstemp";
static char __pyx_k__n_cigar[] = "n_cigar";
-static char __pyx_k__options[] = "options";
-static char __pyx_k__overlap[] = "overlap";
static char __pyx_k__pileups[] = "pileups";
-static char __pyx_k__q_indel[] = "q_indel";
-static char __pyx_k__r_indel[] = "r_indel";
static char __pyx_k__release[] = "release";
static char __pyx_k__restore[] = "restore";
-static char __pyx_k__rowiter[] = "rowiter";
static char __pyx_k__samfile[] = "samfile";
-static char __pyx_k__seq_len[] = "seq_len";
static char __pyx_k__setfile[] = "setfile";
static char __pyx_k__stepper[] = "stepper";
static char __pyx_k__streams[] = "streams";
-static char __pyx_k__DictType[] = "DictType";
static char __pyx_k__KeyError[] = "KeyError";
static char __pyx_k__O_WRONLY[] = "O_WRONLY";
static char __pyx_k____dict__[] = "__dict__";
+static char __pyx_k____exit__[] = "__exit__";
static char __pyx_k____init__[] = "__init__";
static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
-static char __pyx_k___is_head[] = "_is_head";
-static char __pyx_k___is_tail[] = "_is_tail";
-static char __pyx_k___logfile[] = "_logfile";
static char __pyx_k__calcsize[] = "calcsize";
static char __pyx_k__callback[] = "callback";
-static char __pyx_k__cap_mapQ[] = "cap_mapQ";
-static char __pyx_k__cnt_anti[] = "cnt_anti";
+static char __pyx_k__check_sq[] = "check_sq";
static char __pyx_k__coverage[] = "coverage";
static char __pyx_k__data_len[] = "data_len";
static char __pyx_k__exc_type[] = "exc_type";
static char __pyx_k__filename[] = "filename";
static char __pyx_k__genotype[] = "genotype";
-static char __pyx_k__getrname[] = "getrname";
-static char __pyx_k__het_rate[] = "het_rate";
-static char __pyx_k__isremote[] = "isremote";
-static char __pyx_k__iterdata[] = "iterdata";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__platform[] = "platform";
static char __pyx_k__samtools[] = "samtools";
static char __pyx_k__stderr_f[] = "stderr_f";
static char __pyx_k__stderr_h[] = "stderr_h";
+static char __pyx_k__stdout_f[] = "stdout_f";
+static char __pyx_k__stdout_h[] = "stdout_h";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__template[] = "template";
+static char __pyx_k__truncate[] = "truncate";
+static char __pyx_k__warnings[] = "warnings";
static char __pyx_k__Fastafile[] = "Fastafile";
-static char __pyx_k__FloatType[] = "FloatType";
-static char __pyx_k__SNPCaller[] = "SNPCaller";
static char __pyx_k__TypeError[] = "TypeError";
-static char __pyx_k___coverage[] = "_coverage";
-static char __pyx_k___delegate[] = "_delegate";
-static char __pyx_k___filename[] = "_filename";
-static char __pyx_k___genotype[] = "_genotype";
+static char __pyx_k____enter__[] = "__enter__";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__alignment[] = "alignment";
+static char __pyx_k__csamtools[] = "csamtools";
+static char __pyx_k__enumerate[] = "enumerate";
static char __pyx_k__exc_value[] = "exc_value";
-static char __pyx_k__fancy_str[] = "fancy_str";
static char __pyx_k__fastafile[] = "fastafile";
static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__max_depth[] = "max_depth";
-static char __pyx_k__min_baseQ[] = "min_baseQ";
-static char __pyx_k__n_targets[] = "n_targets";
static char __pyx_k__pack_into[] = "pack_into";
static char __pyx_k__positions[] = "positions";
static char __pyx_k__readlines[] = "readlines";
static char __pyx_k__setdevice[] = "setdevice";
static char __pyx_k__traceback[] = "traceback";
static char __pyx_k__until_eof[] = "until_eof";
+static char __pyx_k__CIGAR2CODE[] = "CIGAR2CODE";
+static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
-static char __pyx_k___alignment[] = "_alignment";
static char __pyx_k___buildLine[] = "_buildLine";
-static char __pyx_k__reads_diff[] = "reads_diff";
+static char __pyx_k__out_stderr[] = "out_stderr";
+static char __pyx_k__out_stdout[] = "out_stdout";
+static char __pyx_k__references[] = "references";
static char __pyx_k__startswith[] = "startswith";
-static char __pyx_k__target_len[] = "target_len";
static char __pyx_k__AlignedRead[] = "AlignedRead";
-static char __pyx_k__IndelCaller[] = "IndelCaller";
+static char __pyx_k__CIGAR_REGEX[] = "CIGAR_REGEX";
static char __pyx_k__IteratorRow[] = "IteratorRow";
static char __pyx_k__PileupProxy[] = "PileupProxy";
static char __pyx_k__StderrStore[] = "StderrStore";
+static char __pyx_k__add_sq_text[] = "add_sq_text";
static char __pyx_k__collections[] = "collections";
-static char __pyx_k__current_pos[] = "current_pos";
static char __pyx_k__defaultdict[] = "defaultdict";
-static char __pyx_k__getSequence[] = "getSequence";
static char __pyx_k__nreferences[] = "nreferences";
-static char __pyx_k__pileup_iter[] = "pileup_iter";
-static char __pyx_k__reads_first[] = "reads_first";
static char __pyx_k__snp_quality[] = "snp_quality";
-static char __pyx_k__stderr_save[] = "stderr_save";
-static char __pyx_k__target_name[] = "target_name";
+static char __pyx_k__stdout_save[] = "stdout_save";
static char __pyx_k__IndexedReads[] = "IndexedReads";
static char __pyx_k__PileupColumn[] = "PileupColumn";
-static char __pyx_k___buildHeader[] = "_buildHeader";
static char __pyx_k___parseRegion[] = "_parseRegion";
-static char __pyx_k___snp_quality[] = "_snp_quality";
-static char __pyx_k__addReference[] = "addReference";
-static char __pyx_k__catch_stderr[] = "catch_stderr";
static char __pyx_k__catch_stdout[] = "catch_stdout";
-static char __pyx_k__first_allele[] = "first_allele";
-static char __pyx_k__hasReference[] = "hasReference";
-static char __pyx_k__n_haplotypes[] = "n_haplotypes";
-static char __pyx_k__owns_samfile[] = "owns_samfile";
-static char __pyx_k__reads_second[] = "reads_second";
+static char __pyx_k__check_header[] = "check_header";
+static char __pyx_k__version_info[] = "version_info";
static char __pyx_k__OverflowError[] = "OverflowError";
static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS";
-static char __pyx_k__second_allele[] = "second_allele";
+static char __pyx_k__AttributeError[] = "AttributeError";
static char __pyx_k__IteratorColumn[] = "IteratorColumn";
-static char __pyx_k__IteratorRowAll[] = "IteratorRowAll";
static char __pyx_k__readAndRelease[] = "readAndRelease";
static char __pyx_k__reference_base[] = "reference_base";
static char __pyx_k__referencenames[] = "referencenames";
-static char __pyx_k___reference_base[] = "_reference_base";
-static char __pyx_k__iterator_column[] = "iterator_column";
static char __pyx_k__mapping_quality[] = "mapping_quality";
-static char __pyx_k__IteratorSNPCalls[] = "IteratorSNPCalls";
static char __pyx_k____getattribute__[] = "__getattribute__";
static char __pyx_k__referencelengths[] = "referencelengths";
-static char __pyx_k__IteratorRowRegion[] = "IteratorRowRegion";
static char __pyx_k__consensus_quality[] = "consensus_quality";
-static char __pyx_k__setupIteratorData[] = "setupIteratorData";
-static char __pyx_k__IteratorIndelCalls[] = "IteratorIndelCalls";
-static char __pyx_k__IteratorRowAllRefs[] = "IteratorRowAllRefs";
static char __pyx_k__StderrStoreWindows[] = "StderrStoreWindows";
+static char __pyx_k__UnicodeDecodeError[] = "UnicodeDecodeError";
static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER";
static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES";
-static char __pyx_k___consensus_quality[] = "_consensus_quality";
static char __pyx_k___samtools_dispatch[] = "_samtools_dispatch";
+static char __pyx_k__getdefaultencoding[] = "getdefaultencoding";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
-static PyObject *__pyx_kp_s_1;
+static PyObject *__pyx_kp_u_1;
static PyObject *__pyx_kp_s_10;
static PyObject *__pyx_kp_s_100;
-static PyObject *__pyx_kp_s_101;
static PyObject *__pyx_kp_s_102;
-static PyObject *__pyx_n_s_103;
static PyObject *__pyx_kp_s_104;
static PyObject *__pyx_kp_s_105;
static PyObject *__pyx_kp_s_107;
static PyObject *__pyx_kp_s_108;
static PyObject *__pyx_kp_s_109;
-static PyObject *__pyx_kp_s_11;
static PyObject *__pyx_kp_s_110;
static PyObject *__pyx_kp_s_111;
-static PyObject *__pyx_kp_s_112;
static PyObject *__pyx_kp_s_113;
-static PyObject *__pyx_kp_s_12;
+static PyObject *__pyx_kp_s_116;
+static PyObject *__pyx_kp_s_119;
+static PyObject *__pyx_kp_s_125;
+static PyObject *__pyx_kp_s_126;
+static PyObject *__pyx_kp_s_127;
+static PyObject *__pyx_kp_s_129;
+static PyObject *__pyx_kp_s_13;
+static PyObject *__pyx_kp_s_135;
+static PyObject *__pyx_kp_s_136;
+static PyObject *__pyx_kp_s_137;
+static PyObject *__pyx_kp_s_138;
+static PyObject *__pyx_kp_s_140;
+static PyObject *__pyx_kp_s_141;
+static PyObject *__pyx_kp_s_145;
+static PyObject *__pyx_n_s_147;
+static PyObject *__pyx_kp_s_148;
+static PyObject *__pyx_kp_s_149;
static PyObject *__pyx_kp_s_15;
+static PyObject *__pyx_kp_s_150;
+static PyObject *__pyx_kp_s_151;
+static PyObject *__pyx_kp_s_152;
+static PyObject *__pyx_kp_s_153;
+static PyObject *__pyx_kp_s_154;
+static PyObject *__pyx_kp_s_155;
+static PyObject *__pyx_kp_s_156;
+static PyObject *__pyx_kp_s_157;
+static PyObject *__pyx_kp_s_158;
+static PyObject *__pyx_kp_s_159;
+static PyObject *__pyx_kp_b_16;
static PyObject *__pyx_kp_s_16;
+static PyObject *__pyx_kp_s_160;
+static PyObject *__pyx_kp_s_161;
+static PyObject *__pyx_kp_s_162;
+static PyObject *__pyx_kp_s_163;
+static PyObject *__pyx_kp_s_164;
+static PyObject *__pyx_kp_s_165;
+static PyObject *__pyx_kp_s_166;
+static PyObject *__pyx_kp_s_167;
+static PyObject *__pyx_kp_s_168;
+static PyObject *__pyx_kp_s_169;
+static PyObject *__pyx_kp_s_17;
+static PyObject *__pyx_kp_s_170;
+static PyObject *__pyx_kp_s_171;
static PyObject *__pyx_kp_s_173;
-static PyObject *__pyx_kp_s_174;
-static PyObject *__pyx_kp_s_175;
-static PyObject *__pyx_kp_s_176;
-static PyObject *__pyx_kp_u_177;
-static PyObject *__pyx_kp_u_178;
-static PyObject *__pyx_kp_u_179;
+static PyObject *__pyx_kp_s_177;
+static PyObject *__pyx_kp_s_178;
+static PyObject *__pyx_kp_s_179;
static PyObject *__pyx_kp_s_18;
-static PyObject *__pyx_kp_u_180;
-static PyObject *__pyx_kp_u_181;
-static PyObject *__pyx_kp_u_182;
-static PyObject *__pyx_kp_u_183;
-static PyObject *__pyx_kp_u_184;
-static PyObject *__pyx_kp_u_185;
-static PyObject *__pyx_kp_u_186;
-static PyObject *__pyx_kp_u_187;
-static PyObject *__pyx_kp_u_188;
-static PyObject *__pyx_kp_u_189;
+static PyObject *__pyx_kp_s_185;
+static PyObject *__pyx_kp_s_186;
static PyObject *__pyx_kp_s_19;
-static PyObject *__pyx_kp_u_190;
-static PyObject *__pyx_kp_u_191;
-static PyObject *__pyx_kp_u_192;
-static PyObject *__pyx_kp_u_193;
-static PyObject *__pyx_kp_u_194;
-static PyObject *__pyx_kp_u_195;
-static PyObject *__pyx_kp_u_196;
-static PyObject *__pyx_kp_u_197;
-static PyObject *__pyx_kp_u_198;
-static PyObject *__pyx_kp_u_199;
-static PyObject *__pyx_kp_s_2;
-static PyObject *__pyx_kp_s_20;
-static PyObject *__pyx_n_s_200;
-static PyObject *__pyx_kp_u_201;
-static PyObject *__pyx_kp_u_202;
-static PyObject *__pyx_kp_u_203;
-static PyObject *__pyx_n_s_204;
-static PyObject *__pyx_kp_u_205;
-static PyObject *__pyx_n_s_206;
-static PyObject *__pyx_kp_u_207;
-static PyObject *__pyx_kp_u_208;
-static PyObject *__pyx_kp_u_209;
-static PyObject *__pyx_kp_s_21;
-static PyObject *__pyx_kp_u_210;
-static PyObject *__pyx_kp_u_211;
-static PyObject *__pyx_kp_u_212;
-static PyObject *__pyx_kp_u_213;
-static PyObject *__pyx_kp_u_214;
-static PyObject *__pyx_kp_u_215;
-static PyObject *__pyx_kp_u_216;
-static PyObject *__pyx_kp_u_217;
-static PyObject *__pyx_kp_u_218;
-static PyObject *__pyx_kp_u_219;
-static PyObject *__pyx_kp_s_22;
-static PyObject *__pyx_kp_u_220;
-static PyObject *__pyx_kp_s_23;
static PyObject *__pyx_kp_s_24;
-static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_kp_s_26;
-static PyObject *__pyx_kp_s_27;
-static PyObject *__pyx_kp_s_28;
-static PyObject *__pyx_kp_s_3;
+static PyObject *__pyx_n_s_249;
+static PyObject *__pyx_kp_s_251;
+static PyObject *__pyx_kp_s_256;
+static PyObject *__pyx_kp_s_257;
+static PyObject *__pyx_kp_s_266;
+static PyObject *__pyx_kp_s_273;
+static PyObject *__pyx_kp_s_29;
+static PyObject *__pyx_kp_s_290;
+static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_kp_s_32;
static PyObject *__pyx_kp_s_34;
static PyObject *__pyx_kp_s_35;
static PyObject *__pyx_kp_s_36;
-static PyObject *__pyx_kp_s_37;
+static PyObject *__pyx_kp_b_37;
static PyObject *__pyx_kp_s_38;
-static PyObject *__pyx_kp_s_4;
-static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_41;
-static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
-static PyObject *__pyx_kp_s_44;
static PyObject *__pyx_kp_s_45;
static PyObject *__pyx_kp_s_46;
-static PyObject *__pyx_kp_s_47;
static PyObject *__pyx_kp_s_48;
-static PyObject *__pyx_kp_s_49;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_kp_s_50;
-static PyObject *__pyx_kp_s_51;
-static PyObject *__pyx_kp_s_52;
-static PyObject *__pyx_kp_s_53;
-static PyObject *__pyx_kp_s_54;
-static PyObject *__pyx_kp_s_55;
static PyObject *__pyx_kp_s_56;
-static PyObject *__pyx_kp_s_57;
-static PyObject *__pyx_kp_s_59;
+static PyObject *__pyx_kp_s_58;
static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_kp_s_61;
+static PyObject *__pyx_kp_s_60;
static PyObject *__pyx_kp_s_62;
-static PyObject *__pyx_n_s_63;
static PyObject *__pyx_kp_s_64;
-static PyObject *__pyx_kp_s_65;
static PyObject *__pyx_kp_s_66;
-static PyObject *__pyx_kp_s_67;
-static PyObject *__pyx_kp_s_68;
static PyObject *__pyx_kp_s_69;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_70;
static PyObject *__pyx_kp_s_71;
-static PyObject *__pyx_kp_s_72;
-static PyObject *__pyx_kp_s_73;
-static PyObject *__pyx_kp_s_74;
-static PyObject *__pyx_kp_s_75;
static PyObject *__pyx_kp_s_76;
-static PyObject *__pyx_kp_s_77;
-static PyObject *__pyx_kp_s_78;
static PyObject *__pyx_kp_s_79;
-static PyObject *__pyx_kp_s_8;
-static PyObject *__pyx_kp_s_80;
-static PyObject *__pyx_kp_s_81;
static PyObject *__pyx_kp_s_82;
-static PyObject *__pyx_kp_s_83;
-static PyObject *__pyx_kp_s_84;
static PyObject *__pyx_kp_s_85;
-static PyObject *__pyx_kp_s_86;
-static PyObject *__pyx_kp_s_87;
-static PyObject *__pyx_kp_s_88;
-static PyObject *__pyx_kp_s_89;
static PyObject *__pyx_kp_s_9;
-static PyObject *__pyx_kp_s_90;
-static PyObject *__pyx_kp_s_91;
static PyObject *__pyx_kp_s_92;
-static PyObject *__pyx_kp_s_93;
-static PyObject *__pyx_kp_s_94;
static PyObject *__pyx_kp_s_95;
-static PyObject *__pyx_kp_s_96;
-static PyObject *__pyx_kp_s_97;
+static PyObject *__pyx_kp_s__2scB;
+static PyObject *__pyx_kp_s__2scH;
+static PyObject *__pyx_kp_s__2scI;
+static PyObject *__pyx_kp_s__2scb;
+static PyObject *__pyx_kp_s__2scc;
+static PyObject *__pyx_kp_s__2scf;
+static PyObject *__pyx_kp_s__2sch;
+static PyObject *__pyx_kp_s__2sci;
static PyObject *__pyx_n_s__A;
static PyObject *__pyx_n_s__AS;
static PyObject *__pyx_n_s__AlignedRead;
+static PyObject *__pyx_n_s__AttributeError;
+static PyObject *__pyx_n_s__B;
static PyObject *__pyx_n_s__C;
+static PyObject *__pyx_n_s__CIGAR2CODE;
+static PyObject *__pyx_n_s__CIGAR_REGEX;
static PyObject *__pyx_n_s__CL;
static PyObject *__pyx_n_s__CN;
static PyObject *__pyx_n_s__CO;
static PyObject *__pyx_n_s__D;
static PyObject *__pyx_n_s__DS;
static PyObject *__pyx_n_s__DT;
-static PyObject *__pyx_n_s__DictType;
static PyObject *__pyx_n_s__F;
+static PyObject *__pyx_n_s__FO;
static PyObject *__pyx_n_s__Fastafile;
-static PyObject *__pyx_n_s__FloatType;
static PyObject *__pyx_n_s__GO;
+static PyObject *__pyx_n_s__H;
static PyObject *__pyx_n_s__HD;
static PyObject *__pyx_n_s__I;
static PyObject *__pyx_n_s__ID;
static PyObject *__pyx_n_s__IOError;
-static PyObject *__pyx_n_s__IndelCaller;
+static PyObject *__pyx_n_s__IS_PYTHON3;
static PyObject *__pyx_n_s__IndexedReads;
-static PyObject *__pyx_n_s__IntType;
static PyObject *__pyx_n_s__IteratorColumn;
-static PyObject *__pyx_n_s__IteratorIndelCalls;
static PyObject *__pyx_n_s__IteratorRow;
-static PyObject *__pyx_n_s__IteratorRowAll;
-static PyObject *__pyx_n_s__IteratorRowAllRefs;
-static PyObject *__pyx_n_s__IteratorRowRegion;
-static PyObject *__pyx_n_s__IteratorSNPCalls;
+static PyObject *__pyx_n_s__KS;
static PyObject *__pyx_n_s__KeyError;
static PyObject *__pyx_n_s__LB;
static PyObject *__pyx_n_s__LN;
static PyObject *__pyx_n_s__M5;
static PyObject *__pyx_n_s__NotImplementedError;
+static PyObject *__pyx_n_s__OSError;
static PyObject *__pyx_n_s__O_CREAT;
static PyObject *__pyx_n_s__O_WRONLY;
static PyObject *__pyx_n_s__Outs;
static PyObject *__pyx_n_s__S;
static PyObject *__pyx_n_s__SM;
static PyObject *__pyx_n_s__SN;
-static PyObject *__pyx_n_s__SNPCaller;
static PyObject *__pyx_n_s__SO;
static PyObject *__pyx_n_s__SP;
static PyObject *__pyx_n_s__SQ;
static PyObject *__pyx_n_s__StopIteration;
static PyObject *__pyx_n_s__TypeError;
static PyObject *__pyx_n_s__UR;
+static PyObject *__pyx_n_s__UnicodeDecodeError;
static PyObject *__pyx_n_s__VALID_HEADERS;
static PyObject *__pyx_n_s__VALID_HEADER_FIELDS;
static PyObject *__pyx_n_s__VALID_HEADER_ORDER;
static PyObject *__pyx_n_s____all__;
static PyObject *__pyx_n_s____del__;
static PyObject *__pyx_n_s____dict__;
+static PyObject *__pyx_n_s____enter__;
+static PyObject *__pyx_n_s____exit__;
static PyObject *__pyx_n_s____getattribute__;
static PyObject *__pyx_n_s____init__;
static PyObject *__pyx_n_s____main__;
-static PyObject *__pyx_n_s____next__;
static PyObject *__pyx_n_s____str__;
static PyObject *__pyx_n_s____test__;
-static PyObject *__pyx_n_s___alignment;
-static PyObject *__pyx_n_s___buildHeader;
static PyObject *__pyx_n_s___buildLine;
-static PyObject *__pyx_n_s___call;
-static PyObject *__pyx_n_s___consensus_quality;
-static PyObject *__pyx_n_s___coverage;
-static PyObject *__pyx_n_s___delegate;
-static PyObject *__pyx_n_s___filename;
-static PyObject *__pyx_n_s___genotype;
static PyObject *__pyx_n_s___hasIndex;
-static PyObject *__pyx_n_s___indel;
static PyObject *__pyx_n_s___isOpen;
-static PyObject *__pyx_n_s___is_del;
-static PyObject *__pyx_n_s___is_head;
-static PyObject *__pyx_n_s___is_tail;
-static PyObject *__pyx_n_s___level;
-static PyObject *__pyx_n_s___logfile;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
-static PyObject *__pyx_n_s___pos;
-static PyObject *__pyx_n_s___qpos;
-static PyObject *__pyx_n_s___r;
-static PyObject *__pyx_n_s___reference_base;
static PyObject *__pyx_n_s___samtools_dispatch;
-static PyObject *__pyx_n_s___snp_quality;
-static PyObject *__pyx_n_s___tid;
-static PyObject *__pyx_n_s__addReference;
+static PyObject *__pyx_n_s__a;
+static PyObject *__pyx_n_s__add_sq_text;
static PyObject *__pyx_n_s__alignment;
static PyObject *__pyx_n_s__all;
static PyObject *__pyx_n_s__args;
+static PyObject *__pyx_n_s__ascii;
static PyObject *__pyx_n_s__b;
-static PyObject *__pyx_n_s__bam;
static PyObject *__pyx_n_s__beg;
static PyObject *__pyx_n_s__bin;
static PyObject *__pyx_n_s__bqual;
-static PyObject *__pyx_n_s__build;
static PyObject *__pyx_n_s__c;
static PyObject *__pyx_n_s__calcsize;
-static PyObject *__pyx_n_s__call;
static PyObject *__pyx_n_s__callback;
-static PyObject *__pyx_n_s__cap_mapQ;
-static PyObject *__pyx_n_s__catch_stderr;
+static PyObject *__pyx_n_s__cargs;
static PyObject *__pyx_n_s__catch_stdout;
+static PyObject *__pyx_n_s__check_header;
+static PyObject *__pyx_n_s__check_sq;
static PyObject *__pyx_n_s__chr;
static PyObject *__pyx_n_s__cigar;
static PyObject *__pyx_n_s__close;
-static PyObject *__pyx_n_s__cmp;
-static PyObject *__pyx_n_s__cnext;
-static PyObject *__pyx_n_s__cnt1;
-static PyObject *__pyx_n_s__cnt2;
-static PyObject *__pyx_n_s__cnt_anti;
static PyObject *__pyx_n_s__collections;
-static PyObject *__pyx_n_s__compare;
+static PyObject *__pyx_n_s__compile;
static PyObject *__pyx_n_s__consensus_quality;
-static PyObject *__pyx_n_s__core;
-static PyObject *__pyx_n_s__count;
static PyObject *__pyx_n_s__coverage;
+static PyObject *__pyx_n_s__csamtools;
static PyObject *__pyx_n_s__ctypes;
-static PyObject *__pyx_n_s__current_pos;
static PyObject *__pyx_n_s__d;
-static PyObject *__pyx_n_s__data;
static PyObject *__pyx_n_s__data_len;
+static PyObject *__pyx_n_s__decode;
static PyObject *__pyx_n_s__defaultdict;
-static PyObject *__pyx_n_s__devnull;
static PyObject *__pyx_n_s__dup;
static PyObject *__pyx_n_s__dup2;
+static PyObject *__pyx_n_s__encode;
static PyObject *__pyx_n_s__end;
-static PyObject *__pyx_n_s__errmod;
+static PyObject *__pyx_n_s__enumerate;
static PyObject *__pyx_n_s__exc_type;
static PyObject *__pyx_n_s__exc_value;
static PyObject *__pyx_n_s__exists;
+static PyObject *__pyx_n_s__extend;
static PyObject *__pyx_n_s__f;
-static PyObject *__pyx_n_s__fancy_str;
static PyObject *__pyx_n_s__fastafile;
static PyObject *__pyx_n_s__fd;
-static PyObject *__pyx_n_s__fetch;
static PyObject *__pyx_n_s__fields;
static PyObject *__pyx_n_s__filename;
static PyObject *__pyx_n_s__fileno;
-static PyObject *__pyx_n_s__first_allele;
+static PyObject *__pyx_n_s__findall;
static PyObject *__pyx_n_s__flag;
static PyObject *__pyx_n_s__flush;
-static PyObject *__pyx_n_s__fp;
static PyObject *__pyx_n_s__genotype;
-static PyObject *__pyx_n_s__getSequence;
-static PyObject *__pyx_n_s__getrname;
+static PyObject *__pyx_n_s__getdefaultencoding;
static PyObject *__pyx_n_s__gettid;
-static PyObject *__pyx_n_s__hasReference;
-static PyObject *__pyx_n_s__hash;
+static PyObject *__pyx_n_s__h;
static PyObject *__pyx_n_s__header;
-static PyObject *__pyx_n_s__het_rate;
static PyObject *__pyx_n_s__i;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__indel;
-static PyObject *__pyx_n_s__indel1;
-static PyObject *__pyx_n_s__indel2;
static PyObject *__pyx_n_s__index;
+static PyObject *__pyx_n_s__inf;
static PyObject *__pyx_n_s__is_del;
static PyObject *__pyx_n_s__is_head;
static PyObject *__pyx_n_s__is_tail;
-static PyObject *__pyx_n_s__isbam;
static PyObject *__pyx_n_s__isize;
-static PyObject *__pyx_n_s__isremote;
+static PyObject *__pyx_n_s__islower;
static PyObject *__pyx_n_s__isupper;
-static PyObject *__pyx_n_s__iter;
-static PyObject *__pyx_n_s__iterator_column;
-static PyObject *__pyx_n_s__iterdata;
+static PyObject *__pyx_n_s__items;
static PyObject *__pyx_n_s__itertools;
static PyObject *__pyx_n_s__join;
static PyObject *__pyx_n_s__l_aux;
static PyObject *__pyx_n_s__l_qname;
static PyObject *__pyx_n_s__l_qseq;
-static PyObject *__pyx_n_s__l_text;
+static PyObject *__pyx_n_s__lengths;
static PyObject *__pyx_n_s__level;
static PyObject *__pyx_n_s__m_data;
static PyObject *__pyx_n_s__map;
static PyObject *__pyx_n_s__mapping_quality;
static PyObject *__pyx_n_s__mapq;
static PyObject *__pyx_n_s__mask;
-static PyObject *__pyx_n_s__mate;
+static PyObject *__pyx_n_s__max;
static PyObject *__pyx_n_s__max_depth;
static PyObject *__pyx_n_s__method;
-static PyObject *__pyx_n_s__min_baseQ;
+static PyObject *__pyx_n_s__min;
static PyObject *__pyx_n_s__mkstemp;
static PyObject *__pyx_n_s__mode;
static PyObject *__pyx_n_s__mpos;
static PyObject *__pyx_n_s__mtid;
static PyObject *__pyx_n_s__n;
static PyObject *__pyx_n_s__n_cigar;
-static PyObject *__pyx_n_s__n_hap;
-static PyObject *__pyx_n_s__n_haplotypes;
-static PyObject *__pyx_n_s__n_plp;
-static PyObject *__pyx_n_s__n_pu;
-static PyObject *__pyx_n_s__n_targets;
-static PyObject *__pyx_n_s__name;
static PyObject *__pyx_n_s__nextiter;
static PyObject *__pyx_n_s__nreferences;
static PyObject *__pyx_n_s__object;
+static PyObject *__pyx_n_s__ofd;
static PyObject *__pyx_n_s__offset;
static PyObject *__pyx_n_s__open;
-static PyObject *__pyx_n_s__opt;
-static PyObject *__pyx_n_s__options;
+static PyObject *__pyx_n_s__ord;
static PyObject *__pyx_n_s__os;
-static PyObject *__pyx_n_s__overlap;
-static PyObject *__pyx_n_s__owns_samfile;
+static PyObject *__pyx_n_s__out_stderr;
+static PyObject *__pyx_n_s__out_stdout;
static PyObject *__pyx_n_s__pack_into;
static PyObject *__pyx_n_s__path;
-static PyObject *__pyx_n_s__pileup;
-static PyObject *__pyx_n_s__pileup_iter;
static PyObject *__pyx_n_s__pileups;
static PyObject *__pyx_n_s__platform;
-static PyObject *__pyx_n_s__plp;
static PyObject *__pyx_n_s__port;
static PyObject *__pyx_n_s__pos;
static PyObject *__pyx_n_s__positions;
-static PyObject *__pyx_n_s__q_cns;
-static PyObject *__pyx_n_s__q_indel;
-static PyObject *__pyx_n_s__q_r;
-static PyObject *__pyx_n_s__q_ref;
static PyObject *__pyx_n_s__qname;
static PyObject *__pyx_n_s__qpos;
static PyObject *__pyx_n_s__qseq;
static PyObject *__pyx_n_s__qual;
+static PyObject *__pyx_n_b__r;
static PyObject *__pyx_n_s__r;
-static PyObject *__pyx_n_s__r_indel;
-static PyObject *__pyx_n_s__range;
+static PyObject *__pyx_n_s__rU;
static PyObject *__pyx_n_s__raw;
+static PyObject *__pyx_n_b__rb;
static PyObject *__pyx_n_s__rb;
static PyObject *__pyx_n_s__re;
+static PyObject *__pyx_n_s__read;
static PyObject *__pyx_n_s__readAndRelease;
static PyObject *__pyx_n_s__readlines;
-static PyObject *__pyx_n_s__reads_diff;
-static PyObject *__pyx_n_s__reads_first;
-static PyObject *__pyx_n_s__reads_second;
static PyObject *__pyx_n_s__record;
static PyObject *__pyx_n_s__reference;
static PyObject *__pyx_n_s__reference_base;
static PyObject *__pyx_n_s__referencelengths;
static PyObject *__pyx_n_s__referencenames;
+static PyObject *__pyx_n_s__references;
static PyObject *__pyx_n_s__region;
static PyObject *__pyx_n_s__release;
static PyObject *__pyx_n_s__remove;
static PyObject *__pyx_n_s__reopen;
-static PyObject *__pyx_n_s__reset;
static PyObject *__pyx_n_s__restore;
static PyObject *__pyx_n_s__retval;
-static PyObject *__pyx_n_s__rg2lib;
static PyObject *__pyx_n_s__rlen;
static PyObject *__pyx_n_s__rname;
-static PyObject *__pyx_n_s__rowiter;
static PyObject *__pyx_n_s__s;
static PyObject *__pyx_n_s__samfile;
static PyObject *__pyx_n_s__samtools;
-static PyObject *__pyx_n_s__second_allele;
static PyObject *__pyx_n_s__seek;
static PyObject *__pyx_n_s__self;
static PyObject *__pyx_n_s__seq;
-static PyObject *__pyx_n_s__seq_len;
static PyObject *__pyx_n_s__setdevice;
static PyObject *__pyx_n_s__setfd;
static PyObject *__pyx_n_s__setfile;
-static PyObject *__pyx_n_s__setupIteratorData;
static PyObject *__pyx_n_s__snp_quality;
+static PyObject *__pyx_n_s__sorted;
static PyObject *__pyx_n_s__split;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__stderr;
static PyObject *__pyx_n_s__stderr_f;
static PyObject *__pyx_n_s__stderr_h;
-static PyObject *__pyx_n_s__stderr_save;
static PyObject *__pyx_n_s__stdout;
+static PyObject *__pyx_n_s__stdout_f;
+static PyObject *__pyx_n_s__stdout_h;
+static PyObject *__pyx_n_s__stdout_save;
static PyObject *__pyx_n_s__stepper;
static PyObject *__pyx_n_s__streams;
static PyObject *__pyx_n_s__strip;
static PyObject *__pyx_n_s__sys;
static PyObject *__pyx_n_s__system;
static PyObject *__pyx_n_s__tags;
-static PyObject *__pyx_n_s__target_len;
-static PyObject *__pyx_n_s__target_name;
-static PyObject *__pyx_n_s__tell;
static PyObject *__pyx_n_s__tempfile;
static PyObject *__pyx_n_s__template;
static PyObject *__pyx_n_s__text;
-static PyObject *__pyx_n_s__theta;
static PyObject *__pyx_n_s__tid;
static PyObject *__pyx_n_s__traceback;
+static PyObject *__pyx_n_s__truncate;
static PyObject *__pyx_n_s__types;
static PyObject *__pyx_n_s__until_eof;
+static PyObject *__pyx_n_s__version_info;
static PyObject *__pyx_n_s__view;
static PyObject *__pyx_n_s__w;
+static PyObject *__pyx_n_s__warn;
+static PyObject *__pyx_n_s__warnings;
static PyObject *__pyx_n_s__wb;
static PyObject *__pyx_n_s__wbu;
static PyObject *__pyx_n_s__wh;
static PyObject *__pyx_n_s__where;
static PyObject *__pyx_n_s__write;
-static PyObject *__pyx_n_s__x;
+static PyObject *__pyx_n_s__zip;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_2;
+static PyObject *__pyx_int_3;
static PyObject *__pyx_int_4;
static PyObject *__pyx_int_8;
-static PyObject *__pyx_int_13;
static PyObject *__pyx_int_16;
static PyObject *__pyx_int_32;
-static PyObject *__pyx_int_40;
-static PyObject *__pyx_int_60;
static PyObject *__pyx_int_64;
static PyObject *__pyx_int_128;
static PyObject *__pyx_int_255;
static PyObject *__pyx_int_neg_127;
static PyObject *__pyx_int_0660;
static PyObject *__pyx_int_1024;
+static PyObject *__pyx_int_8000;
static PyObject *__pyx_int_65535;
static PyObject *__pyx_int_neg_32767;
static PyObject *__pyx_int_536870912;
static PyObject *__pyx_int_4294967295;
static PyObject *__pyx_int_neg_2147483648;
-static PyObject *__pyx_k_29;
-static PyObject *__pyx_k_39;
-static int __pyx_k_58;
-static PyObject *__pyx_k_98;
-static PyObject *__pyx_k_99;
+static PyObject *__pyx_k_21;
+static PyObject *__pyx_k_22;
+static PyObject *__pyx_k_23;
+static PyObject *__pyx_k_54;
+static PyObject *__pyx_k_73;
+static int __pyx_k_128;
+static PyObject *__pyx_k_176;
+static PyObject *__pyx_k_tuple_2;
+static PyObject *__pyx_k_tuple_4;
+static PyObject *__pyx_k_tuple_8;
+static PyObject *__pyx_k_tuple_11;
+static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_14;
+static PyObject *__pyx_k_tuple_20;
+static PyObject *__pyx_k_tuple_25;
+static PyObject *__pyx_k_tuple_39;
+static PyObject *__pyx_k_tuple_40;
+static PyObject *__pyx_k_tuple_42;
+static PyObject *__pyx_k_tuple_44;
+static PyObject *__pyx_k_tuple_47;
+static PyObject *__pyx_k_tuple_49;
+static PyObject *__pyx_k_tuple_51;
+static PyObject *__pyx_k_tuple_52;
+static PyObject *__pyx_k_tuple_53;
+static PyObject *__pyx_k_tuple_55;
+static PyObject *__pyx_k_tuple_57;
+static PyObject *__pyx_k_tuple_59;
+static PyObject *__pyx_k_tuple_61;
+static PyObject *__pyx_k_tuple_63;
+static PyObject *__pyx_k_tuple_65;
+static PyObject *__pyx_k_tuple_67;
+static PyObject *__pyx_k_tuple_68;
+static PyObject *__pyx_k_tuple_72;
+static PyObject *__pyx_k_tuple_74;
+static PyObject *__pyx_k_tuple_75;
+static PyObject *__pyx_k_tuple_77;
+static PyObject *__pyx_k_tuple_78;
+static PyObject *__pyx_k_tuple_80;
+static PyObject *__pyx_k_tuple_81;
+static PyObject *__pyx_k_tuple_83;
+static PyObject *__pyx_k_tuple_84;
+static PyObject *__pyx_k_tuple_86;
+static PyObject *__pyx_k_tuple_87;
+static PyObject *__pyx_k_tuple_88;
+static PyObject *__pyx_k_tuple_89;
+static PyObject *__pyx_k_tuple_90;
+static PyObject *__pyx_k_tuple_91;
+static PyObject *__pyx_k_tuple_93;
+static PyObject *__pyx_k_tuple_94;
+static PyObject *__pyx_k_tuple_96;
+static PyObject *__pyx_k_tuple_97;
+static PyObject *__pyx_k_tuple_98;
+static PyObject *__pyx_k_tuple_99;
+static PyObject *__pyx_k_tuple_101;
+static PyObject *__pyx_k_tuple_103;
+static PyObject *__pyx_k_tuple_106;
+static PyObject *__pyx_k_tuple_112;
+static PyObject *__pyx_k_tuple_114;
+static PyObject *__pyx_k_tuple_115;
+static PyObject *__pyx_k_tuple_117;
+static PyObject *__pyx_k_tuple_118;
+static PyObject *__pyx_k_tuple_120;
+static PyObject *__pyx_k_tuple_121;
+static PyObject *__pyx_k_tuple_122;
+static PyObject *__pyx_k_tuple_123;
+static PyObject *__pyx_k_tuple_124;
+static PyObject *__pyx_k_tuple_130;
+static PyObject *__pyx_k_tuple_131;
+static PyObject *__pyx_k_tuple_133;
+static PyObject *__pyx_k_tuple_134;
+static PyObject *__pyx_k_tuple_139;
+static PyObject *__pyx_k_tuple_142;
+static PyObject *__pyx_k_tuple_143;
+static PyObject *__pyx_k_tuple_144;
+static PyObject *__pyx_k_tuple_146;
+static PyObject *__pyx_k_tuple_172;
+static PyObject *__pyx_k_tuple_174;
+static PyObject *__pyx_k_tuple_175;
+static PyObject *__pyx_k_tuple_180;
+static PyObject *__pyx_k_tuple_181;
+static PyObject *__pyx_k_tuple_182;
+static PyObject *__pyx_k_tuple_183;
+static PyObject *__pyx_k_tuple_184;
+static PyObject *__pyx_k_tuple_252;
+static PyObject *__pyx_k_tuple_254;
+static PyObject *__pyx_k_tuple_258;
+static PyObject *__pyx_k_tuple_260;
+static PyObject *__pyx_k_tuple_262;
+static PyObject *__pyx_k_tuple_264;
+static PyObject *__pyx_k_tuple_267;
+static PyObject *__pyx_k_tuple_269;
+static PyObject *__pyx_k_tuple_271;
+static PyObject *__pyx_k_tuple_274;
+static PyObject *__pyx_k_tuple_275;
+static PyObject *__pyx_k_tuple_276;
+static PyObject *__pyx_k_tuple_277;
+static PyObject *__pyx_k_tuple_278;
+static PyObject *__pyx_k_tuple_279;
+static PyObject *__pyx_k_tuple_281;
+static PyObject *__pyx_k_tuple_282;
+static PyObject *__pyx_k_tuple_284;
+static PyObject *__pyx_k_tuple_286;
+static PyObject *__pyx_k_tuple_288;
+static PyObject *__pyx_k_tuple_291;
+static PyObject *__pyx_k_codeobj_255;
+static PyObject *__pyx_k_codeobj_259;
+static PyObject *__pyx_k_codeobj_261;
+static PyObject *__pyx_k_codeobj_263;
+static PyObject *__pyx_k_codeobj_265;
+static PyObject *__pyx_k_codeobj_268;
+static PyObject *__pyx_k_codeobj_270;
+static PyObject *__pyx_k_codeobj_272;
+static PyObject *__pyx_k_codeobj_280;
+static PyObject *__pyx_k_codeobj_283;
+static PyObject *__pyx_k_codeobj_285;
+static PyObject *__pyx_k_codeobj_287;
+static PyObject *__pyx_k_codeobj_289;
+static PyObject *__pyx_k_codeobj_292;
+static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+
+/* "csamtools.pyx":140
+ * cdef char* CODE2CIGAR= "MIDNSHP=X"
+ * if IS_PYTHON3:
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
+ */
+
+static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("genexpr", 0);
+ __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
+ if (unlikely(!__pyx_cur_scope)) {
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ }
+ __Pyx_GOTREF(__pyx_cur_scope);
+ __Pyx_TraceCall("genexpr", __pyx_f[0], 140);
+ {
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_9csamtools_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) gen;
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":76
- * #####################################################################
- * cdef class AlignedRead
- * cdef makeAlignedRead(bam1_t * src): # <<<<<<<<<<<<<<
- * '''enter src into AlignedRead.'''
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
- */
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_DECREF(((PyObject *)__pyx_cur_scope));
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
-static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
- struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
+static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+{
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope = ((struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makeAlignedRead");
- __Pyx_TraceCall("makeAlignedRead", __pyx_f[0], 76);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":78
- * cdef makeAlignedRead(bam1_t * src):
- * '''enter src into AlignedRead.'''
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
- * dest._delegate = bam_dup1(src)
- * return dest
- */
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
- __pyx_t_1 = 0;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *(*__pyx_t_4)(PyObject *);
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("None", 0);
+ switch (__pyx_generator->resume_label) {
+ case 0: goto __pyx_L3_first_run;
+ case 1: goto __pyx_L6_resume_from_yield;
+ default: /* CPython raises the right error here */
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ }
+ __pyx_L3_first_run:;
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_int_0);
+ __pyx_t_1 = __pyx_int_0;
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ for (;;) {
+ {
+ __pyx_t_2 = __pyx_t_4(__pyx_t_3);
+ if (unlikely(!__pyx_t_2)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_2);
+ }
+ __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_y);
+ __Pyx_XDECREF(__pyx_cur_scope->__pyx_v_y);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_cur_scope->__pyx_v_y = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_x);
+ __Pyx_XDECREF(__pyx_cur_scope->__pyx_v_x);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_cur_scope->__pyx_v_x = __pyx_t_1;
+ __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1);
+ __pyx_t_1 = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
+ __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
+ __Pyx_INCREF(__pyx_cur_scope->__pyx_v_x);
+ PyList_SET_ITEM(__pyx_t_2, 1, __pyx_cur_scope->__pyx_v_x);
+ __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_x);
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ __Pyx_XGIVEREF(__pyx_t_1);
+ __pyx_cur_scope->__pyx_t_0 = __pyx_t_1;
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __pyx_cur_scope->__pyx_t_1 = __pyx_t_3;
+ __pyx_cur_scope->__pyx_t_2 = __pyx_t_4;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ /* return from generator, yielding value */
+ __pyx_generator->resume_label = 1;
+ return __pyx_r;
+ __pyx_L6_resume_from_yield:;
+ __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
+ __pyx_cur_scope->__pyx_t_0 = 0;
+ __Pyx_XGOTREF(__pyx_t_1);
+ __pyx_t_3 = __pyx_cur_scope->__pyx_t_1;
+ __pyx_cur_scope->__pyx_t_1 = 0;
+ __Pyx_XGOTREF(__pyx_t_3);
+ __pyx_t_4 = __pyx_cur_scope->__pyx_t_2;
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ PyErr_SetNone(PyExc_StopIteration);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_generator->resume_label = -1;
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+}
+static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":79
- * '''enter src into AlignedRead.'''
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
- * dest._delegate = bam_dup1(src) # <<<<<<<<<<<<<<
- * return dest
+/* "csamtools.pyx":142
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
*
*/
- __pyx_v_dest->_delegate = bam_dup1(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":80
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
- * dest._delegate = bam_dup1(src)
- * return dest # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("genexpr", 0);
+ __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
+ if (unlikely(!__pyx_cur_scope)) {
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ }
+ __Pyx_GOTREF(__pyx_cur_scope);
+ __Pyx_TraceCall("genexpr", __pyx_f[0], 142);
+ {
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_9csamtools_7generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) gen;
+ }
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_DECREF(((PyObject *)__pyx_cur_scope));
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+{
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_generator->closure);
+ PyObject *__pyx_r = NULL;
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *(*__pyx_t_4)(PyObject *);
+ PyObject *__pyx_t_5 = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("None", 0);
+ switch (__pyx_generator->resume_label) {
+ case 0: goto __pyx_L3_first_run;
+ case 1: goto __pyx_L6_resume_from_yield;
+ default: /* CPython raises the right error here */
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ }
+ __pyx_L3_first_run:;
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_int_0);
+ __pyx_t_1 = __pyx_int_0;
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ for (;;) {
+ {
+ __pyx_t_2 = __pyx_t_4(__pyx_t_3);
+ if (unlikely(!__pyx_t_2)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_2);
+ }
+ __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_y);
+ __Pyx_XDECREF(__pyx_cur_scope->__pyx_v_y);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_cur_scope->__pyx_v_y = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_x);
+ __Pyx_XDECREF(__pyx_cur_scope->__pyx_v_x);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_cur_scope->__pyx_v_x = __pyx_t_1;
+ __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1);
+ __pyx_t_1 = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
+ __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ord, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __Pyx_INCREF(__pyx_cur_scope->__pyx_v_x);
+ PyList_SET_ITEM(__pyx_t_2, 1, __pyx_cur_scope->__pyx_v_x);
+ __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_x);
+ __pyx_t_5 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ __Pyx_XGIVEREF(__pyx_t_1);
+ __pyx_cur_scope->__pyx_t_0 = __pyx_t_1;
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __pyx_cur_scope->__pyx_t_1 = __pyx_t_3;
+ __pyx_cur_scope->__pyx_t_2 = __pyx_t_4;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ /* return from generator, yielding value */
+ __pyx_generator->resume_label = 1;
+ return __pyx_r;
+ __pyx_L6_resume_from_yield:;
+ __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
+ __pyx_cur_scope->__pyx_t_0 = 0;
+ __Pyx_XGOTREF(__pyx_t_1);
+ __pyx_t_3 = __pyx_cur_scope->__pyx_t_1;
+ __pyx_cur_scope->__pyx_t_1 = 0;
+ __Pyx_XGOTREF(__pyx_t_3);
+ __pyx_t_4 = __pyx_cur_scope->__pyx_t_2;
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ PyErr_SetNone(PyExc_StopIteration);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_generator->resume_label = -1;
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+}
+
+/* "csamtools.pyx":24
+ * ########################################################################
+ * IS_PYTHON3 = PY_MAJOR_VERSION >= 3
+ * cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<<
+ * if PY_MAJOR_VERSION < 3:
+ * return s[:length]
+ */
+
+static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("from_string_and_size", 0);
+ __Pyx_TraceCall("from_string_and_size", __pyx_f[0], 24);
+
+ /* "csamtools.pyx":25
+ * IS_PYTHON3 = PY_MAJOR_VERSION >= 3
+ * cdef from_string_and_size(char* s, size_t length):
+ * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
+ * return s[:length]
+ * else:
+ */
+ __pyx_t_1 = (PY_MAJOR_VERSION < 3);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":26
+ * cdef from_string_and_size(char* s, size_t length):
+ * if PY_MAJOR_VERSION < 3:
+ * return s[:length] # <<<<<<<<<<<<<<
+ * else:
+ * return s[:length].decode("ascii")
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":28
+ * return s[:length]
+ * else:
+ * return s[:length].decode("ascii") # <<<<<<<<<<<<<<
*
- * cdef class PileupProxy
+ * # filename encoding (copied from lxml.etree.pyx)
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_dest));
- __pyx_r = ((PyObject *)__pyx_v_dest);
- goto __pyx_L0;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ }
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.makeAlignedRead");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
- __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":83
+/* "csamtools.pyx":41
+ * #_C_FILENAME_ENCODING = <char*>_FILENAME_ENCODING
*
- * cdef class PileupProxy
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ): # <<<<<<<<<<<<<<
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
- * dest.plp = plp
+ * cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<<
+ * u"""Make sure a filename is 8-bit encoded (or None).
+ * """
*/
-static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
- struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_dest = 0;
+static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupProxy");
- __Pyx_TraceCall("makePileupProxy", __pyx_f[0], 83);
+ __Pyx_RefNannySetupContext("_my_encodeFilename", 0);
+ __Pyx_TraceCall("_my_encodeFilename", __pyx_f[0], 41);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":84
- * cdef class PileupProxy
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) # <<<<<<<<<<<<<<
- * dest.plp = plp
- * dest.tid = tid
+ /* "csamtools.pyx":44
+ * u"""Make sure a filename is 8-bit encoded (or None).
+ * """
+ * if filename is None: # <<<<<<<<<<<<<<
+ * return None
+ * elif PyBytes_Check(filename):
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_1 = (__pyx_v_filename == Py_None);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":85
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
- * dest.plp = plp # <<<<<<<<<<<<<<
- * dest.tid = tid
- * dest.pos = pos
+ /* "csamtools.pyx":45
+ * """
+ * if filename is None:
+ * return None # <<<<<<<<<<<<<<
+ * elif PyBytes_Check(filename):
+ * return filename
*/
- __pyx_v_dest->plp = __pyx_v_plp;
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ __Pyx_INCREF(Py_None);
+ __pyx_r = ((PyObject*)Py_None);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":86
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
- * dest.plp = plp
- * dest.tid = tid # <<<<<<<<<<<<<<
- * dest.pos = pos
- * dest.n = n
+ /* "csamtools.pyx":46
+ * if filename is None:
+ * return None
+ * elif PyBytes_Check(filename): # <<<<<<<<<<<<<<
+ * return filename
+ * elif PyUnicode_Check(filename):
*/
- __pyx_v_dest->tid = __pyx_v_tid;
+ __pyx_t_1 = PyBytes_Check(__pyx_v_filename);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":87
- * dest.plp = plp
- * dest.tid = tid
- * dest.pos = pos # <<<<<<<<<<<<<<
- * dest.n = n
- * return dest
+ /* "csamtools.pyx":47
+ * return None
+ * elif PyBytes_Check(filename):
+ * return filename # <<<<<<<<<<<<<<
+ * elif PyUnicode_Check(filename):
+ * return filename.encode(_FILENAME_ENCODING)
+ */
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ if (!(likely(PyBytes_CheckExact(__pyx_v_filename))||((__pyx_v_filename) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_filename)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_v_filename);
+ __pyx_r = ((PyObject*)__pyx_v_filename);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+
+ /* "csamtools.pyx":48
+ * elif PyBytes_Check(filename):
+ * return filename
+ * elif PyUnicode_Check(filename): # <<<<<<<<<<<<<<
+ * return filename.encode(_FILENAME_ENCODING)
+ * else:
*/
- __pyx_v_dest->pos = __pyx_v_pos;
+ __pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":88
- * dest.tid = tid
- * dest.pos = pos
- * dest.n = n # <<<<<<<<<<<<<<
- * return dest
- *
+ /* "csamtools.pyx":49
+ * return filename
+ * elif PyUnicode_Check(filename):
+ * return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<<
+ * else:
+ * raise TypeError, u"Argument must be string or unicode."
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_n); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(((PyObject *)__pyx_v_dest), __pyx_n_s__n, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ if (!(likely(PyBytes_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = ((PyObject*)__pyx_t_4);
+ __pyx_t_4 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":89
- * dest.pos = pos
- * dest.n = n
- * return dest # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":51
+ * return filename.encode(_FILENAME_ENCODING)
+ * else:
+ * raise TypeError, u"Argument must be string or unicode." # <<<<<<<<<<<<<<
+ *
*
- * cdef class PileupRead
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_dest));
- __pyx_r = ((PyObject *)__pyx_v_dest);
- goto __pyx_L0;
+ __Pyx_Raise(__pyx_builtin_TypeError, ((PyObject *)__pyx_kp_u_1), 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L3:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.makePileupProxy");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
- __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":92
+/* "csamtools.pyx":54
*
- * cdef class PileupRead
- * cdef makePileupRead( bam_pileup1_t * src ): # <<<<<<<<<<<<<<
- * '''fill a PileupRead object from a bam_pileup1_t * object.'''
- * cdef PileupRead dest = PileupRead.__new__(PileupRead)
+ *
+ * cdef bytes _force_bytes(object s): # <<<<<<<<<<<<<<
+ * u"""convert string or unicode object to bytes, assuming ascii encoding.
+ * """
*/
-static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
- struct __pyx_obj_9csamtools_PileupRead *__pyx_v_dest = 0;
+static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupRead");
- __Pyx_TraceCall("makePileupRead", __pyx_f[0], 92);
+ __Pyx_RefNannySetupContext("_force_bytes", 0);
+ __Pyx_TraceCall("_force_bytes", __pyx_f[0], 54);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":94
- * cdef makePileupRead( bam_pileup1_t * src ):
- * '''fill a PileupRead object from a bam_pileup1_t * object.'''
- * cdef PileupRead dest = PileupRead.__new__(PileupRead) # <<<<<<<<<<<<<<
- * dest._alignment = makeAlignedRead( src.b )
- * dest._qpos = src.qpos
+ /* "csamtools.pyx":57
+ * u"""convert string or unicode object to bytes, assuming ascii encoding.
+ * """
+ * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
+ * return s
+ * elif s is None:
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupRead *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_1 = (PY_MAJOR_VERSION < 3);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":95
- * '''fill a PileupRead object from a bam_pileup1_t * object.'''
- * cdef PileupRead dest = PileupRead.__new__(PileupRead)
- * dest._alignment = makeAlignedRead( src.b ) # <<<<<<<<<<<<<<
- * dest._qpos = src.qpos
- * dest._indel = src.indel
+ /* "csamtools.pyx":58
+ * """
+ * if PY_MAJOR_VERSION < 3:
+ * return s # <<<<<<<<<<<<<<
+ * elif s is None:
+ * return None
*/
- __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_src->b); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(__pyx_v_dest->_alignment);
- __Pyx_DECREF(((PyObject *)__pyx_v_dest->_alignment));
- __pyx_v_dest->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ if (!(likely(PyBytes_CheckExact(__pyx_v_s))||((__pyx_v_s) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_s)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_v_s);
+ __pyx_r = ((PyObject*)__pyx_v_s);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":96
- * cdef PileupRead dest = PileupRead.__new__(PileupRead)
- * dest._alignment = makeAlignedRead( src.b )
- * dest._qpos = src.qpos # <<<<<<<<<<<<<<
- * dest._indel = src.indel
- * dest._level = src.level
+ /* "csamtools.pyx":59
+ * if PY_MAJOR_VERSION < 3:
+ * return s
+ * elif s is None: # <<<<<<<<<<<<<<
+ * return None
+ * elif PyBytes_Check(s):
*/
- __pyx_v_dest->_qpos = __pyx_v_src->qpos;
+ __pyx_t_1 = (__pyx_v_s == Py_None);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":97
- * dest._alignment = makeAlignedRead( src.b )
- * dest._qpos = src.qpos
- * dest._indel = src.indel # <<<<<<<<<<<<<<
- * dest._level = src.level
- * dest._is_del = src.is_del
+ /* "csamtools.pyx":60
+ * return s
+ * elif s is None:
+ * return None # <<<<<<<<<<<<<<
+ * elif PyBytes_Check(s):
+ * return s
*/
- __pyx_v_dest->_indel = __pyx_v_src->indel;
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ __Pyx_INCREF(Py_None);
+ __pyx_r = ((PyObject*)Py_None);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":98
- * dest._qpos = src.qpos
- * dest._indel = src.indel
- * dest._level = src.level # <<<<<<<<<<<<<<
- * dest._is_del = src.is_del
- * dest._is_head = src.is_head
+ /* "csamtools.pyx":61
+ * elif s is None:
+ * return None
+ * elif PyBytes_Check(s): # <<<<<<<<<<<<<<
+ * return s
+ * elif PyUnicode_Check(s):
*/
- __pyx_v_dest->_level = __pyx_v_src->level;
+ __pyx_t_1 = PyBytes_Check(__pyx_v_s);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":99
- * dest._indel = src.indel
- * dest._level = src.level
- * dest._is_del = src.is_del # <<<<<<<<<<<<<<
- * dest._is_head = src.is_head
- * dest._is_tail = src.is_tail
+ /* "csamtools.pyx":62
+ * return None
+ * elif PyBytes_Check(s):
+ * return s # <<<<<<<<<<<<<<
+ * elif PyUnicode_Check(s):
+ * return s.encode('ascii')
*/
- __pyx_v_dest->_is_del = __pyx_v_src->is_del;
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ if (!(likely(PyBytes_CheckExact(__pyx_v_s))||((__pyx_v_s) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_s)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_v_s);
+ __pyx_r = ((PyObject*)__pyx_v_s);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":100
- * dest._level = src.level
- * dest._is_del = src.is_del
- * dest._is_head = src.is_head # <<<<<<<<<<<<<<
- * dest._is_tail = src.is_tail
- * return dest
+ /* "csamtools.pyx":63
+ * elif PyBytes_Check(s):
+ * return s
+ * elif PyUnicode_Check(s): # <<<<<<<<<<<<<<
+ * return s.encode('ascii')
+ * else:
*/
- __pyx_v_dest->_is_head = __pyx_v_src->is_head;
+ __pyx_t_1 = PyUnicode_Check(__pyx_v_s);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":101
- * dest._is_del = src.is_del
- * dest._is_head = src.is_head
- * dest._is_tail = src.is_tail # <<<<<<<<<<<<<<
- * return dest
- *
+ /* "csamtools.pyx":64
+ * return s
+ * elif PyUnicode_Check(s):
+ * return s.encode('ascii') # <<<<<<<<<<<<<<
+ * else:
+ * raise TypeError, u"Argument must be string, bytes or unicode."
*/
- __pyx_v_dest->_is_tail = __pyx_v_src->is_tail;
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_s, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (!(likely(PyBytes_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":102
- * dest._is_head = src.is_head
- * dest._is_tail = src.is_tail
- * return dest # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":66
+ * return s.encode('ascii')
+ * else:
+ * raise TypeError, u"Argument must be string, bytes or unicode." # <<<<<<<<<<<<<<
*
- * #####################################################################
+ * cdef inline bytes _force_cmdline_bytes(object s):
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_dest));
- __pyx_r = ((PyObject *)__pyx_v_dest);
- goto __pyx_L0;
+ __Pyx_Raise(__pyx_builtin_TypeError, ((PyObject *)__pyx_kp_u_3), 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L3:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.makePileupRead");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
- __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":109
- * ## Generic callbacks for inserting python callbacks.
- * #####################################################################
- * cdef int fetch_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
- * '''callback for bam_fetch.
+/* "csamtools.pyx":68
+ * raise TypeError, u"Argument must be string, bytes or unicode."
+ *
+ * cdef inline bytes _force_cmdline_bytes(object s): # <<<<<<<<<<<<<<
+ * return _force_bytes(s)
*
*/
-static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
- PyObject *__pyx_v_a;
- int __pyx_r;
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *__pyx_v_s) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch_callback");
- __Pyx_TraceCall("fetch_callback", __pyx_f[0], 109);
- __pyx_v_a = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("_force_cmdline_bytes", 0);
+ __Pyx_TraceCall("_force_cmdline_bytes", __pyx_f[0], 68);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":114
- * calls function in *f* with a new :class:`AlignedRead` object as parameter.
- * '''
- * a = makeAlignedRead( alignment ) # <<<<<<<<<<<<<<
- * (<object>f)(a)
+ /* "csamtools.pyx":69
*
- */
- __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_alignment); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":115
- * '''
- * a = makeAlignedRead( alignment )
- * (<object>f)(a) # <<<<<<<<<<<<<<
+ * cdef inline bytes _force_cmdline_bytes(object s):
+ * return _force_bytes(s) # <<<<<<<<<<<<<<
*
- * class PileupColumn(object):
+ * cdef _charptr_to_str(char* s):
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(((PyObject *)__pyx_r));
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_a);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_a);
- __Pyx_GIVEREF(__pyx_v_a);
- __pyx_t_2 = PyObject_Call(((PyObject *)__pyx_v_f), __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = ((PyObject*)__pyx_t_1);
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- __pyx_r = 0;
+ __pyx_r = ((PyObject*)Py_None); __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_WriteUnraisable("csamtools.fetch_callback");
+ __Pyx_AddTraceback("csamtools._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_a);
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":130
- * list of reads (:class:`pysam.PileupRead`) aligned to this column
- * '''
- * def __str__(self): # <<<<<<<<<<<<<<
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" + "\n".join( map(str, self.pileups) )
+/* "csamtools.pyx":71
+ * return _force_bytes(s)
+ *
+ * cdef _charptr_to_str(char* s): # <<<<<<<<<<<<<<
+ * if PY_MAJOR_VERSION < 3:
+ * return s
*/
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn___str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pf_9csamtools_12PileupColumn___str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)};
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 130);
- __pyx_self = __pyx_self;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":131
- * '''
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
- * "\n" + "\n".join( map(str, self.pileups) )
- *
- */
- __Pyx_XDECREF(__pyx_r);
+ __Pyx_RefNannySetupContext("_charptr_to_str", 0);
+ __Pyx_TraceCall("_charptr_to_str", __pyx_f[0], 71);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":132
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":72
*
- * cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f):
+ * cdef _charptr_to_str(char* s):
+ * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
+ * return s
+ * else:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = (PY_MAJOR_VERSION < 3);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":131
- * '''
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
- * "\n" + "\n".join( map(str, self.pileups) )
- *
+ /* "csamtools.pyx":73
+ * cdef _charptr_to_str(char* s):
+ * if PY_MAJOR_VERSION < 3:
+ * return s # <<<<<<<<<<<<<<
+ * else:
+ * return s.decode("ascii")
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_map, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_s); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":132
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":75
+ * return s
+ * else:
+ * return s.decode("ascii") # <<<<<<<<<<<<<<
*
- * cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f):
+ * cdef _force_str(object s):
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_map, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_5, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Add(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ }
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.PileupColumn.__str__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":134
- * "\n" + "\n".join( map(str, self.pileups) )
- *
- * cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f): # <<<<<<<<<<<<<<
- * '''callback for pileup.
+/* "csamtools.pyx":77
+ * return s.decode("ascii")
*
+ * cdef _force_str(object s): # <<<<<<<<<<<<<<
+ * """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
+ * if s is None:
*/
-static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __pyx_v_pos, int __pyx_v_n, bam_pileup1_t *__pyx_v_pl, void *__pyx_v_f) {
- PyObject *__pyx_v_p;
- PyObject *__pyx_v_pileups;
- int __pyx_v_x;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
+static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_callback");
- __Pyx_TraceCall("pileup_callback", __pyx_f[0], 134);
- __pyx_v_p = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_pileups = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("_force_str", 0);
+ __Pyx_TraceCall("_force_str", __pyx_f[0], 77);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":151
- * '''
- *
- * p = PileupColumn() # <<<<<<<<<<<<<<
- * p.tid = tid
- * p.pos = pos
+ /* "csamtools.pyx":79
+ * cdef _force_str(object s):
+ * """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
+ * if s is None: # <<<<<<<<<<<<<<
+ * return None
+ * if PY_MAJOR_VERSION < 3:
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__PileupColumn); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_p);
- __pyx_v_p = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":152
- *
- * p = PileupColumn()
- * p.tid = tid # <<<<<<<<<<<<<<
- * p.pos = pos
- * p.n = n
- */
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__tid, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_1 = (__pyx_v_s == Py_None);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":153
- * p = PileupColumn()
- * p.tid = tid
- * p.pos = pos # <<<<<<<<<<<<<<
- * p.n = n
- * pileups = []
+ /* "csamtools.pyx":80
+ * """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
+ * if s is None:
+ * return None # <<<<<<<<<<<<<<
+ * if PY_MAJOR_VERSION < 3:
+ * return s
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pos, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":154
- * p.tid = tid
- * p.pos = pos
- * p.n = n # <<<<<<<<<<<<<<
- * pileups = []
- *
+ /* "csamtools.pyx":81
+ * if s is None:
+ * return None
+ * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
+ * return s
+ * elif PyBytes_Check(s):
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_n); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__n, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_1 = (PY_MAJOR_VERSION < 3);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":155
- * p.pos = pos
- * p.n = n
- * pileups = [] # <<<<<<<<<<<<<<
- *
- * cdef int x
+ /* "csamtools.pyx":82
+ * return None
+ * if PY_MAJOR_VERSION < 3:
+ * return s # <<<<<<<<<<<<<<
+ * elif PyBytes_Check(s):
+ * return s.decode('ascii')
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(((PyObject *)__pyx_v_pileups));
- __pyx_v_pileups = __pyx_t_2;
- __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(__pyx_v_s);
+ __pyx_r = __pyx_v_s;
+ goto __pyx_L0;
+ goto __pyx_L4;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":158
- *
- * cdef int x
- * for x from 0 <= x < n: # <<<<<<<<<<<<<<
- * pileups.append( makePileupRead( &(pl[x]) ) )
- * p.pileups = pileups
+ /* "csamtools.pyx":83
+ * if PY_MAJOR_VERSION < 3:
+ * return s
+ * elif PyBytes_Check(s): # <<<<<<<<<<<<<<
+ * return s.decode('ascii')
+ * else:
*/
- __pyx_t_3 = __pyx_v_n;
- for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+ __pyx_t_1 = PyBytes_Check(__pyx_v_s);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":159
- * cdef int x
- * for x from 0 <= x < n:
- * pileups.append( makePileupRead( &(pl[x]) ) ) # <<<<<<<<<<<<<<
- * p.pileups = pileups
- *
+ /* "csamtools.pyx":84
+ * return s
+ * elif PyBytes_Check(s):
+ * return s.decode('ascii') # <<<<<<<<<<<<<<
+ * else:
+ * # assume unicode
*/
- if (unlikely(__pyx_v_pileups == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __pyx_f_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_s, __pyx_n_s__decode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyList_Append(((PyObject *)__pyx_v_pileups), __pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
}
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":160
- * for x from 0 <= x < n:
- * pileups.append( makePileupRead( &(pl[x]) ) )
- * p.pileups = pileups # <<<<<<<<<<<<<<
- *
- * (<object>f)(p)
- */
- if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pileups, ((PyObject *)__pyx_v_pileups)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":162
- * p.pileups = pileups
- *
- * (<object>f)(p) # <<<<<<<<<<<<<<
- *
- * cdef int pileup_fetch_callback( bam1_t *b, void *data):
+ /* "csamtools.pyx":87
+ * else:
+ * # assume unicode
+ * return s # <<<<<<<<<<<<<<
+ * ########################################################################
+ * ########################################################################
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_p);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_p);
- __Pyx_GIVEREF(__pyx_v_p);
- __pyx_t_1 = PyObject_Call(((PyObject *)__pyx_v_f), __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(__pyx_v_s);
+ __pyx_r = __pyx_v_s;
+ goto __pyx_L0;
+ }
+ __pyx_L4:;
- __pyx_r = 0;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_WriteUnraisable("csamtools.pileup_callback");
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_p);
- __Pyx_DECREF(__pyx_v_pileups);
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":164
- * (<object>f)(p)
- *
- * cdef int pileup_fetch_callback( bam1_t *b, void *data): # <<<<<<<<<<<<<<
- * '''callback for bam_fetch.
- *
+/* "csamtools.pyx":160
+ * #####################################################################
+ * cdef class AlignedRead
+ * cdef makeAlignedRead(bam1_t * src): # <<<<<<<<<<<<<<
+ * '''enter src into AlignedRead.'''
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
-static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__pyx_v_data) {
- bam_plbuf_t *__pyx_v_buf;
- int __pyx_r;
+static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
+ struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_fetch_callback");
- __Pyx_TraceCall("pileup_fetch_callback", __pyx_f[0], 164);
+ __Pyx_RefNannySetupContext("makeAlignedRead", 0);
+ __Pyx_TraceCall("makeAlignedRead", __pyx_f[0], 160);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":170
- * '''
- * cdef bam_plbuf_t * buf
- * buf = <bam_plbuf_t*>data # <<<<<<<<<<<<<<
- * bam_plbuf_push(b, buf)
- * return 0
+ /* "csamtools.pyx":162
+ * cdef makeAlignedRead(bam1_t * src):
+ * '''enter src into AlignedRead.'''
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
+ * dest._delegate = bam_dup1(src)
+ * return dest
*/
- __pyx_v_buf = ((bam_plbuf_t *)__pyx_v_data);
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":171
- * cdef bam_plbuf_t * buf
- * buf = <bam_plbuf_t*>data
- * bam_plbuf_push(b, buf) # <<<<<<<<<<<<<<
- * return 0
+ /* "csamtools.pyx":163
+ * '''enter src into AlignedRead.'''
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
+ * dest._delegate = bam_dup1(src) # <<<<<<<<<<<<<<
+ * return dest
*
*/
- bam_plbuf_push(__pyx_v_b, __pyx_v_buf);
+ __pyx_v_dest->_delegate = bam_dup1(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":172
- * buf = <bam_plbuf_t*>data
- * bam_plbuf_push(b, buf)
- * return 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":164
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
+ * dest._delegate = bam_dup1(src)
+ * return dest # <<<<<<<<<<<<<<
*
- * class StderrStore():
+ * cdef class PileupProxy
*/
- __pyx_r = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_dest));
+ __pyx_r = ((PyObject *)__pyx_v_dest);
goto __pyx_L0;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.makeAlignedRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XDECREF((PyObject *)__pyx_v_dest);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":178
- * stderr is captured.
- * '''
- * def __init__(self): # <<<<<<<<<<<<<<
- * return
- * self.stderr_h, self.stderr_f = tempfile.mkstemp()
+/* "csamtools.pyx":167
+ *
+ * cdef class PileupProxy
+ * cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ): # <<<<<<<<<<<<<<
+ * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ * dest.plp = plp
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___init__)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
+ struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 178);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("makePileupProxy", 0);
+ __Pyx_TraceCall("makePileupProxy", __pyx_f[0], 167);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":179
- * '''
- * def __init__(self):
- * return # <<<<<<<<<<<<<<
- * self.stderr_h, self.stderr_f = tempfile.mkstemp()
- * self.stderr_save = Outs( sys.stderr.fileno() )
+ /* "csamtools.pyx":168
+ * cdef class PileupProxy
+ * cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
+ * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) # <<<<<<<<<<<<<<
+ * dest.plp = plp
+ * dest.tid = tid
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":180
- * def __init__(self):
- * return
- * self.stderr_h, self.stderr_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
- * self.stderr_save = Outs( sys.stderr.fileno() )
- * self.stderr_save.setfd( self.stderr_h )
+ /* "csamtools.pyx":169
+ * cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
+ * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ * dest.plp = plp # <<<<<<<<<<<<<<
+ * dest.tid = tid
+ * dest.pos = pos
+ */
+ __pyx_v_dest->plp = __pyx_v_plp;
+
+ /* "csamtools.pyx":170
+ * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ * dest.plp = plp
+ * dest.tid = tid # <<<<<<<<<<<<<<
+ * dest.pos = pos
+ * dest.n = n
+ */
+ __pyx_v_dest->tid = __pyx_v_tid;
+
+ /* "csamtools.pyx":171
+ * dest.plp = plp
+ * dest.tid = tid
+ * dest.pos = pos # <<<<<<<<<<<<<<
+ * dest.n = n
+ * return dest
+ */
+ __pyx_v_dest->pos = __pyx_v_pos;
+
+ /* "csamtools.pyx":172
+ * dest.tid = tid
+ * dest.pos = pos
+ * dest.n = n # <<<<<<<<<<<<<<
+ * return dest
+ *
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_n); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_dest), __pyx_n_s__n, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyTuple_CheckExact(__pyx_t_1) && likely(PyTuple_GET_SIZE(__pyx_t_1) == 2)) {
- PyObject* tuple = __pyx_t_1;
- __pyx_t_2 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__stderr_h, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__stderr_f, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- } else {
- __pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_2 = __Pyx_UnpackItem(__pyx_t_4, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_4, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_EndUnpack(__pyx_t_4, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__stderr_h, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__stderr_f, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":181
- * return
- * self.stderr_h, self.stderr_f = tempfile.mkstemp()
- * self.stderr_save = Outs( sys.stderr.fileno() ) # <<<<<<<<<<<<<<
- * self.stderr_save.setfd( self.stderr_h )
+ /* "csamtools.pyx":173
+ * dest.pos = pos
+ * dest.n = n
+ * return dest # <<<<<<<<<<<<<<
*
+ * cdef class PileupRead
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stderr); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__stderr_save, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":182
- * self.stderr_h, self.stderr_f = tempfile.mkstemp()
- * self.stderr_save = Outs( sys.stderr.fileno() )
- * self.stderr_save.setfd( self.stderr_h ) # <<<<<<<<<<<<<<
- *
- * def readAndRelease( self ):
- */
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_save); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_h); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_dest));
+ __pyx_r = ((PyObject *)__pyx_v_dest);
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.StderrStore.__init__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.makePileupProxy", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
+ __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":184
- * self.stderr_save.setfd( self.stderr_h )
+/* "csamtools.pyx":176
*
- * def readAndRelease( self ): # <<<<<<<<<<<<<<
- * return []
- * self.stderr_save.restore()
+ * cdef class PileupRead
+ * cdef makePileupRead( bam_pileup1_t * src ): # <<<<<<<<<<<<<<
+ * '''fill a PileupRead object from a bam_pileup1_t * object.'''
+ * cdef PileupRead dest = PileupRead.__new__(PileupRead)
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_readAndRelease[] = "StderrStore.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_readAndRelease)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore_readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_v_lines;
+static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
+ struct __pyx_obj_9csamtools_PileupRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease");
- __Pyx_TraceCall("readAndRelease", __pyx_f[0], 184);
- __pyx_self = __pyx_self;
- __pyx_v_lines = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("makePileupRead", 0);
+ __Pyx_TraceCall("makePileupRead", __pyx_f[0], 176);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":185
- *
- * def readAndRelease( self ):
- * return [] # <<<<<<<<<<<<<<
- * self.stderr_save.restore()
- * lines = []
+ /* "csamtools.pyx":178
+ * cdef makePileupRead( bam_pileup1_t * src ):
+ * '''fill a PileupRead object from a bam_pileup1_t * object.'''
+ * cdef PileupRead dest = PileupRead.__new__(PileupRead) # <<<<<<<<<<<<<<
+ * dest._alignment = makeAlignedRead( src.b )
+ * dest._qpos = src.qpos
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupRead *)__pyx_t_1);
__pyx_t_1 = 0;
- goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":186
- * def readAndRelease( self ):
- * return []
- * self.stderr_save.restore() # <<<<<<<<<<<<<<
- * lines = []
- * if os.path.exists(self.stderr_f):
+ /* "csamtools.pyx":179
+ * '''fill a PileupRead object from a bam_pileup1_t * object.'''
+ * cdef PileupRead dest = PileupRead.__new__(PileupRead)
+ * dest._alignment = makeAlignedRead( src.b ) # <<<<<<<<<<<<<<
+ * dest._qpos = src.qpos
+ * dest._indel = src.indel
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_save); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_src->b); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__restore); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_v_dest->_alignment);
+ __Pyx_DECREF(((PyObject *)__pyx_v_dest->_alignment));
+ __pyx_v_dest->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":187
- * return []
- * self.stderr_save.restore()
- * lines = [] # <<<<<<<<<<<<<<
- * if os.path.exists(self.stderr_f):
- * lines = open( self.stderr_f, "r" ).readlines()
+ /* "csamtools.pyx":180
+ * cdef PileupRead dest = PileupRead.__new__(PileupRead)
+ * dest._alignment = makeAlignedRead( src.b )
+ * dest._qpos = src.qpos # <<<<<<<<<<<<<<
+ * dest._indel = src.indel
+ * dest._level = src.level
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_v_lines);
- __pyx_v_lines = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_v_dest->_qpos = __pyx_v_src->qpos;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":188
- * self.stderr_save.restore()
- * lines = []
- * if os.path.exists(self.stderr_f): # <<<<<<<<<<<<<<
- * lines = open( self.stderr_f, "r" ).readlines()
- * os.remove( self.stderr_f )
+ /* "csamtools.pyx":181
+ * dest._alignment = makeAlignedRead( src.b )
+ * dest._qpos = src.qpos
+ * dest._indel = src.indel # <<<<<<<<<<<<<<
+ * dest._level = src.level
+ * dest._is_del = src.is_del
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_4) {
+ __pyx_v_dest->_indel = __pyx_v_src->indel;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":189
- * lines = []
- * if os.path.exists(self.stderr_f):
- * lines = open( self.stderr_f, "r" ).readlines() # <<<<<<<<<<<<<<
- * os.remove( self.stderr_f )
- * return lines
+ /* "csamtools.pyx":182
+ * dest._qpos = src.qpos
+ * dest._indel = src.indel
+ * dest._level = src.level # <<<<<<<<<<<<<<
+ * dest._is_del = src.is_del
+ * dest._is_head = src.is_head
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_open, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__readlines); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_lines);
- __pyx_v_lines = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_dest->_level = __pyx_v_src->level;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":190
- * if os.path.exists(self.stderr_f):
- * lines = open( self.stderr_f, "r" ).readlines()
- * os.remove( self.stderr_f ) # <<<<<<<<<<<<<<
- * return lines
+ /* "csamtools.pyx":183
+ * dest._indel = src.indel
+ * dest._level = src.level
+ * dest._is_del = src.is_del # <<<<<<<<<<<<<<
+ * dest._is_head = src.is_head
+ * dest._is_tail = src.is_tail
+ */
+ __pyx_v_dest->_is_del = __pyx_v_src->is_del;
+
+ /* "csamtools.pyx":184
+ * dest._level = src.level
+ * dest._is_del = src.is_del
+ * dest._is_head = src.is_head # <<<<<<<<<<<<<<
+ * dest._is_tail = src.is_tail
+ * return dest
+ */
+ __pyx_v_dest->_is_head = __pyx_v_src->is_head;
+
+ /* "csamtools.pyx":185
+ * dest._is_del = src.is_del
+ * dest._is_head = src.is_head
+ * dest._is_tail = src.is_tail # <<<<<<<<<<<<<<
+ * return dest
*
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__remove); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_v_dest->_is_tail = __pyx_v_src->is_tail;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":191
- * lines = open( self.stderr_f, "r" ).readlines()
- * os.remove( self.stderr_f )
- * return lines # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":186
+ * dest._is_head = src.is_head
+ * dest._is_tail = src.is_tail
+ * return dest # <<<<<<<<<<<<<<
*
- * def release(self):
+ * cdef convertBinaryTagToList( uint8_t * s ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_lines);
- __pyx_r = __pyx_v_lines;
+ __Pyx_INCREF(((PyObject *)__pyx_v_dest));
+ __pyx_r = ((PyObject *)__pyx_v_dest);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.StderrStore.readAndRelease");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.makePileupRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_lines);
+ __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":193
- * return lines
+/* "csamtools.pyx":188
+ * return dest
*
- * def release(self): # <<<<<<<<<<<<<<
- * return
- * self.stderr_save.restore()
+ * cdef convertBinaryTagToList( uint8_t * s ): # <<<<<<<<<<<<<<
+ * """return bytesize, number of values list of values in s."""
+ * cdef char auxtype
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_release[] = "StderrStore.release(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_release)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore_release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
+ char __pyx_v_auxtype;
+ uint8_t __pyx_v_byte_size;
+ int32_t __pyx_v_nvalues;
+ PyObject *__pyx_v_values = NULL;
+ CYTHON_UNUSED long __pyx_v_x;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_2;
+ int32_t __pyx_t_3;
int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release");
- __Pyx_TraceCall("release", __pyx_f[0], 193);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("convertBinaryTagToList", 0);
+ __Pyx_TraceCall("convertBinaryTagToList", __pyx_f[0], 188);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":194
+ /* "csamtools.pyx":195
*
- * def release(self):
- * return # <<<<<<<<<<<<<<
- * self.stderr_save.restore()
- * if os.path.exists(self.stderr_f):
+ * # get byte size
+ * auxtype = s[0] # <<<<<<<<<<<<<<
+ * byte_size = bam_aux_type2size( auxtype )
+ * s += 1
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
+ __pyx_v_auxtype = (__pyx_v_s[0]);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":195
- * def release(self):
- * return
- * self.stderr_save.restore() # <<<<<<<<<<<<<<
- * if os.path.exists(self.stderr_f):
- * os.remove( self.stderr_f )
+ /* "csamtools.pyx":196
+ * # get byte size
+ * auxtype = s[0]
+ * byte_size = bam_aux_type2size( auxtype ) # <<<<<<<<<<<<<<
+ * s += 1
+ * # get number of values in array
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_save); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__restore); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_byte_size = bam_aux_type2size(__pyx_v_auxtype);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":196
- * return
- * self.stderr_save.restore()
- * if os.path.exists(self.stderr_f): # <<<<<<<<<<<<<<
- * os.remove( self.stderr_f )
- *
+ /* "csamtools.pyx":197
+ * auxtype = s[0]
+ * byte_size = bam_aux_type2size( auxtype )
+ * s += 1 # <<<<<<<<<<<<<<
+ * # get number of values in array
+ * nvalues = (<int32_t*>s)[0]
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = (__pyx_v_s + 1);
+
+ /* "csamtools.pyx":199
+ * s += 1
+ * # get number of values in array
+ * nvalues = (<int32_t*>s)[0] # <<<<<<<<<<<<<<
+ * s += 4
+ * # get values
+ */
+ __pyx_v_nvalues = (((int32_t *)__pyx_v_s)[0]);
+
+ /* "csamtools.pyx":200
+ * # get number of values in array
+ * nvalues = (<int32_t*>s)[0]
+ * s += 4 # <<<<<<<<<<<<<<
+ * # get values
+ * values = []
+ */
+ __pyx_v_s = (__pyx_v_s + 4);
+
+ /* "csamtools.pyx":202
+ * s += 4
+ * # get values
+ * values = [] # <<<<<<<<<<<<<<
+ * if auxtype == 'c':
+ * for x from 0 <= x < nvalues:
+ */
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_4) {
+ __pyx_v_values = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":197
- * self.stderr_save.restore()
- * if os.path.exists(self.stderr_f):
- * os.remove( self.stderr_f ) # <<<<<<<<<<<<<<
- *
- * def __del__(self):
+ /* "csamtools.pyx":203
+ * # get values
+ * values = []
+ * if auxtype == 'c': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<int8_t*>s)[0])
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__remove); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L5;
+ __pyx_t_2 = (__pyx_v_auxtype == 'c');
+ if (__pyx_t_2) {
+
+ /* "csamtools.pyx":204
+ * values = []
+ * if auxtype == 'c':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<int8_t*>s)[0])
+ * s += 1
+ */
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":205
+ * if auxtype == 'c':
+ * for x from 0 <= x < nvalues:
+ * values.append((<int8_t*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 1
+ * elif auxtype == 'C':
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_int8_t((((int8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":206
+ * for x from 0 <= x < nvalues:
+ * values.append((<int8_t*>s)[0])
+ * s += 1 # <<<<<<<<<<<<<<
+ * elif auxtype == 'C':
+ * for x from 0 <= x < nvalues:
+ */
+ __pyx_v_s = (__pyx_v_s + 1);
+ }
+ goto __pyx_L3;
}
- __pyx_L5:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.StderrStore.release");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":207
+ * values.append((<int8_t*>s)[0])
+ * s += 1
+ * elif auxtype == 'C': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint8_t*>s)[0])
+ */
+ __pyx_t_2 = (__pyx_v_auxtype == 'C');
+ if (__pyx_t_2) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":199
- * os.remove( self.stderr_f )
- *
- * def __del__(self): # <<<<<<<<<<<<<<
- * self.release()
- *
+ /* "csamtools.pyx":208
+ * s += 1
+ * elif auxtype == 'C':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<uint8_t*>s)[0])
+ * s += 1
*/
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
-static PyObject *__pyx_pf_9csamtools_11StderrStore___del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore___del__[] = "StderrStore.__del__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore___del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore___del__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___del__)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore___del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__del__");
- __Pyx_TraceCall("__del__", __pyx_f[0], 199);
- __pyx_self = __pyx_self;
+ /* "csamtools.pyx":209
+ * elif auxtype == 'C':
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint8_t*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 1
+ * elif auxtype == 's':
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((((uint8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":200
- *
- * def __del__(self):
- * self.release() # <<<<<<<<<<<<<<
- *
- * class StderrStoreWindows():
+ /* "csamtools.pyx":210
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint8_t*>s)[0])
+ * s += 1 # <<<<<<<<<<<<<<
+ * elif auxtype == 's':
+ * for x from 0 <= x < nvalues:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__release); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_s = (__pyx_v_s + 1);
+ }
+ goto __pyx_L3;
+ }
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.StderrStore.__del__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":211
+ * values.append((<uint8_t*>s)[0])
+ * s += 1
+ * elif auxtype == 's': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<int16_t*>s)[0])
+ */
+ __pyx_t_2 = (__pyx_v_auxtype == 's');
+ if (__pyx_t_2) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":204
- * class StderrStoreWindows():
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass # <<<<<<<<<<<<<<
- * def readAndRelease(self): return []
- * def release(self): pass
+ /* "csamtools.pyx":212
+ * s += 1
+ * elif auxtype == 's':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<int16_t*>s)[0])
+ * s += 2
*/
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows___init__)};
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 204);
- __pyx_self = __pyx_self;
+ /* "csamtools.pyx":213
+ * elif auxtype == 's':
+ * for x from 0 <= x < nvalues:
+ * values.append((<int16_t*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 2
+ * elif auxtype == 'S':
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":214
+ * for x from 0 <= x < nvalues:
+ * values.append((<int16_t*>s)[0])
+ * s += 2 # <<<<<<<<<<<<<<
+ * elif auxtype == 'S':
+ * for x from 0 <= x < nvalues:
+ */
+ __pyx_v_s = (__pyx_v_s + 2);
+ }
+ goto __pyx_L3;
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":205
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass
- * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
- * def release(self): pass
+ /* "csamtools.pyx":215
+ * values.append((<int16_t*>s)[0])
+ * s += 2
+ * elif auxtype == 'S': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint16_t*>s)[0])
+ */
+ __pyx_t_2 = (__pyx_v_auxtype == 'S');
+ if (__pyx_t_2) {
+
+ /* "csamtools.pyx":216
+ * s += 2
+ * elif auxtype == 'S':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<uint16_t*>s)[0])
+ * s += 2
+ */
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":217
+ * elif auxtype == 'S':
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint16_t*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 2
+ * elif auxtype == 'i':
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":218
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint16_t*>s)[0])
+ * s += 2 # <<<<<<<<<<<<<<
+ * elif auxtype == 'i':
+ * for x from 0 <= x < nvalues:
+ */
+ __pyx_v_s = (__pyx_v_s + 2);
+ }
+ goto __pyx_L3;
+ }
+
+ /* "csamtools.pyx":219
+ * values.append((<uint16_t*>s)[0])
+ * s += 2
+ * elif auxtype == 'i': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<int32_t*>s)[0])
+ */
+ __pyx_t_2 = (__pyx_v_auxtype == 'i');
+ if (__pyx_t_2) {
+
+ /* "csamtools.pyx":220
+ * s += 2
+ * elif auxtype == 'i':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<int32_t*>s)[0])
+ * s += 4
+ */
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":221
+ * elif auxtype == 'i':
+ * for x from 0 <= x < nvalues:
+ * values.append((<int32_t*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 4
+ * elif auxtype == 'I':
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t((((int32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":222
+ * for x from 0 <= x < nvalues:
+ * values.append((<int32_t*>s)[0])
+ * s += 4 # <<<<<<<<<<<<<<
+ * elif auxtype == 'I':
+ * for x from 0 <= x < nvalues:
+ */
+ __pyx_v_s = (__pyx_v_s + 4);
+ }
+ goto __pyx_L3;
+ }
+
+ /* "csamtools.pyx":223
+ * values.append((<int32_t*>s)[0])
+ * s += 4
+ * elif auxtype == 'I': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint32_t*>s)[0])
+ */
+ __pyx_t_2 = (__pyx_v_auxtype == 'I');
+ if (__pyx_t_2) {
+
+ /* "csamtools.pyx":224
+ * s += 4
+ * elif auxtype == 'I':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<uint32_t*>s)[0])
+ * s += 4
+ */
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":225
+ * elif auxtype == 'I':
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint32_t*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 4
+ * elif auxtype == 'f':
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t((((uint32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":226
+ * for x from 0 <= x < nvalues:
+ * values.append((<uint32_t*>s)[0])
+ * s += 4 # <<<<<<<<<<<<<<
+ * elif auxtype == 'f':
+ * for x from 0 <= x < nvalues:
+ */
+ __pyx_v_s = (__pyx_v_s + 4);
+ }
+ goto __pyx_L3;
+ }
+
+ /* "csamtools.pyx":227
+ * values.append((<uint32_t*>s)[0])
+ * s += 4
+ * elif auxtype == 'f': # <<<<<<<<<<<<<<
+ * for x from 0 <= x < nvalues:
+ * values.append((<float*>s)[0])
+ */
+ __pyx_t_2 = (__pyx_v_auxtype == 'f');
+ if (__pyx_t_2) {
+
+ /* "csamtools.pyx":228
+ * s += 4
+ * elif auxtype == 'f':
+ * for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
+ * values.append((<float*>s)[0])
+ * s += 4
+ */
+ __pyx_t_3 = __pyx_v_nvalues;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":229
+ * elif auxtype == 'f':
+ * for x from 0 <= x < nvalues:
+ * values.append((<float*>s)[0]) # <<<<<<<<<<<<<<
+ * s += 4
*
*/
+ __pyx_t_1 = PyFloat_FromDouble((((float *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows_readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_readAndRelease)};
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease");
- __Pyx_TraceCall("readAndRelease", __pyx_f[0], 205);
- __pyx_self = __pyx_self;
+ /* "csamtools.pyx":230
+ * for x from 0 <= x < nvalues:
+ * values.append((<float*>s)[0])
+ * s += 4 # <<<<<<<<<<<<<<
+ *
+ * return byte_size, nvalues, values
+ */
+ __pyx_v_s = (__pyx_v_s + 4);
+ }
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":232
+ * s += 4
+ *
+ * return byte_size, nvalues, values # <<<<<<<<<<<<<<
+ *
+ * #####################################################################
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t(__pyx_v_byte_size); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = __Pyx_PyInt_to_py_int32_t(__pyx_v_nvalues); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __Pyx_INCREF(((PyObject *)__pyx_v_values));
+ PyTuple_SET_ITEM(__pyx_t_6, 2, ((PyObject *)__pyx_v_values));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_values));
__pyx_t_1 = 0;
+ __pyx_t_5 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_6);
+ __pyx_t_6 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.StderrStoreWindows.readAndRelease");
- __pyx_r = NULL;
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_AddTraceback("csamtools.convertBinaryTagToList", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_values);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":206
- * def __init__(self): pass
- * def readAndRelease(self): return []
- * def release(self): pass # <<<<<<<<<<<<<<
- *
- * if platform.system()=='Windows':
- */
-
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows_release[] = "StderrStoreWindows.release(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_release)};
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release");
- __Pyx_TraceCall("release", __pyx_f[0], 206);
- __pyx_self = __pyx_self;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":260
- * cdef faidx_t * fastafile
+/* "csamtools.pyx":239
+ * ## Generic callbacks for inserting python callbacks.
+ * #####################################################################
+ * cdef int fetch_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
+ * '''callback for bam_fetch.
*
- * def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
- * self.fastafile = NULL
- * self._filename = NULL
*/
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
+static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+ PyObject *__pyx_v_a = NULL;
int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 260);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":261
- *
- * def __cinit__(self, *args, **kwargs ):
- * self.fastafile = NULL # <<<<<<<<<<<<<<
- * self._filename = NULL
- * self._open( *args, **kwargs )
- */
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
+ __Pyx_RefNannySetupContext("fetch_callback", 0);
+ __Pyx_TraceCall("fetch_callback", __pyx_f[0], 239);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":262
- * def __cinit__(self, *args, **kwargs ):
- * self.fastafile = NULL
- * self._filename = NULL # <<<<<<<<<<<<<<
- * self._open( *args, **kwargs )
+ /* "csamtools.pyx":244
+ * calls function in *f* with a new :class:`AlignedRead` object as parameter.
+ * '''
+ * a = makeAlignedRead( alignment ) # <<<<<<<<<<<<<<
+ * (<object>f)(a)
*
*/
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = NULL;
+ __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_alignment); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_a = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":263
- * self.fastafile = NULL
- * self._filename = NULL
- * self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":245
+ * '''
+ * a = makeAlignedRead( alignment )
+ * (<object>f)(a) # <<<<<<<<<<<<<<
*
- * def _isOpen( self ):
+ * class PileupColumn(object):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_INCREF(__pyx_v_a);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_a);
+ __Pyx_GIVEREF(__pyx_v_a);
+ __pyx_t_2 = PyObject_Call(((PyObject *)__pyx_v_f), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Fastafile.__cinit__");
- __pyx_r = -1;
+ __Pyx_WriteUnraisable("csamtools.fetch_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_args);
- __Pyx_DECREF(__pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_a);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":265
- * self._open( *args, **kwargs )
- *
- * def _isOpen( self ): # <<<<<<<<<<<<<<
- * '''return true if samfile has been opened.'''
- * return self.fastafile != NULL
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn_1__str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pw_9csamtools_12PileupColumn_1__str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)};
+static PyObject *__pyx_pw_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_12PileupColumn___str__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":260
+ * list of reads (:class:`pysam.PileupRead`) aligned to this column
+ * '''
+ * def __str__(self): # <<<<<<<<<<<<<<
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" + "\n".join( map(str, self.pileups) )
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile__isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pf_9csamtools_9Fastafile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen");
- __Pyx_TraceCall("_isOpen", __pyx_f[0], 265);
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 260);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":267
- * def _isOpen( self ):
- * '''return true if samfile has been opened.'''
- * return self.fastafile != NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":261
+ * '''
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
+ * "\n" + "\n".join( map(str, self.pileups) )
*
- * def __len__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":262
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
+ *
+ * cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f):
+ */
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
+
+ /* "csamtools.pyx":261
+ * '''
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
+ * "\n" + "\n".join( map(str, self.pileups) )
+ *
+ */
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_2 = 0;
+ __pyx_t_3 = 0;
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_4 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+
+ /* "csamtools.pyx":262
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
+ *
+ * cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f):
+ */
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyNumber_Add(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Fastafile._isOpen");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("csamtools.PileupColumn.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":269
- * return self.fastafile != NULL
+/* "csamtools.pyx":264
+ * "\n" + "\n".join( map(str, self.pileups) )
+ *
+ * cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f): # <<<<<<<<<<<<<<
+ * '''callback for pileup.
*
- * def __len__(self): # <<<<<<<<<<<<<<
- * if self.fastafile == NULL:
- * raise ValueError( "calling len() on closed file" )
*/
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile___len__(PyObject *__pyx_v_self); /*proto*/
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile___len__(PyObject *__pyx_v_self) {
- Py_ssize_t __pyx_r;
- int __pyx_t_1;
+static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __pyx_v_pos, int __pyx_v_n, bam_pileup1_t *__pyx_v_pl, void *__pyx_v_f) {
+ PyObject *__pyx_v_p = NULL;
+ PyObject *__pyx_v_pileups = NULL;
+ int __pyx_v_x;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__len__");
- __Pyx_TraceCall("__len__", __pyx_f[0], 269);
+ __Pyx_RefNannySetupContext("pileup_callback", 0);
+ __Pyx_TraceCall("pileup_callback", __pyx_f[0], 264);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":270
+ /* "csamtools.pyx":281
+ * '''
*
- * def __len__(self):
- * if self.fastafile == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "calling len() on closed file" )
+ * p = PileupColumn() # <<<<<<<<<<<<<<
+ * p.tid = tid
+ * p.pos = pos
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__PileupColumn); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_p = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":282
*
+ * p = PileupColumn()
+ * p.tid = tid # <<<<<<<<<<<<<<
+ * p.pos = pos
+ * p.n = n
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
- if (__pyx_t_1) {
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__tid, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":271
- * def __len__(self):
- * if self.fastafile == NULL:
- * raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":283
+ * p = PileupColumn()
+ * p.tid = tid
+ * p.pos = pos # <<<<<<<<<<<<<<
+ * p.n = n
+ * pileups = []
+ */
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pos, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":284
+ * p.tid = tid
+ * p.pos = pos
+ * p.n = n # <<<<<<<<<<<<<<
+ * pileups = []
+ *
+ */
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_n); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__n, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":285
+ * p.pos = pos
+ * p.n = n
+ * pileups = [] # <<<<<<<<<<<<<<
+ *
+ * cdef int x
+ */
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_pileups = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":288
+ *
+ * cdef int x
+ * for x from 0 <= x < n: # <<<<<<<<<<<<<<
+ * pileups.append( makePileupRead( &(pl[x]) ) )
+ * p.pileups = pileups
+ */
+ __pyx_t_3 = __pyx_v_n;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":289
+ * cdef int x
+ * for x from 0 <= x < n:
+ * pileups.append( makePileupRead( &(pl[x]) ) ) # <<<<<<<<<<<<<<
+ * p.pileups = pileups
*
- * return faidx_fetch_nseq(self.fastafile)
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_3));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_3));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
}
- __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":273
- * raise ValueError( "calling len() on closed file" )
+ /* "csamtools.pyx":290
+ * for x from 0 <= x < n:
+ * pileups.append( makePileupRead( &(pl[x]) ) )
+ * p.pileups = pileups # <<<<<<<<<<<<<<
*
- * return faidx_fetch_nseq(self.fastafile) # <<<<<<<<<<<<<<
+ * (<object>f)(p)
+ */
+ if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pileups, ((PyObject *)__pyx_v_pileups)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":292
+ * p.pileups = pileups
*
- * def _open( self,
+ * (<object>f)(p) # <<<<<<<<<<<<<<
+ *
+ * cdef int pileup_fetch_callback( bam1_t *b, void *data):
*/
- __pyx_r = faidx_fetch_nseq(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
- goto __pyx_L0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_p);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_p);
+ __Pyx_GIVEREF(__pyx_v_p);
+ __pyx_t_1 = PyObject_Call(((PyObject *)__pyx_v_f), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Fastafile.__len__");
- __pyx_r = -1;
+ __Pyx_WriteUnraisable("csamtools.pileup_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_p);
+ __Pyx_XDECREF(__pyx_v_pileups);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":275
- * return faidx_fetch_nseq(self.fastafile)
+/* "csamtools.pyx":294
+ * (<object>f)(p)
+ *
+ * cdef int pileup_fetch_callback( bam1_t *b, void *data): # <<<<<<<<<<<<<<
+ * '''callback for bam_fetch.
*
- * def _open( self, # <<<<<<<<<<<<<<
- * char * filename ):
- * '''open an indexed fasta file.
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile__open(PyObject *__pyx_v_self, PyObject *__pyx_arg_filename); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile__open[] = "Fastafile._open(self, char *filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
-static PyObject *__pyx_pf_9csamtools_9Fastafile__open(PyObject *__pyx_v_self, PyObject *__pyx_arg_filename) {
- char *__pyx_v_filename;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__pyx_v_data) {
+ bam_plbuf_t *__pyx_v_buf;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open");
- __Pyx_TraceCall("_open", __pyx_f[0], 275);
- assert(__pyx_arg_filename); {
- __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Fastafile._open");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
+ __Pyx_RefNannySetupContext("pileup_fetch_callback", 0);
+ __Pyx_TraceCall("pileup_fetch_callback", __pyx_f[0], 294);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":283
- *
- * # close a previously opened file
- * if self.fastafile != NULL: self.close() # <<<<<<<<<<<<<<
- * if self._filename != NULL: free(self._filename)
- * self._filename = strdup(filename)
+ /* "csamtools.pyx":300
+ * '''
+ * cdef bam_plbuf_t * buf
+ * buf = <bam_plbuf_t*>data # <<<<<<<<<<<<<<
+ * bam_plbuf_push(b, buf)
+ * return 0
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
- if (__pyx_t_1) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_v_buf = ((bam_plbuf_t *)__pyx_v_data);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":284
- * # close a previously opened file
- * if self.fastafile != NULL: self.close()
- * if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
- * self._filename = strdup(filename)
- * self.fastafile = fai_load( filename )
+ /* "csamtools.pyx":301
+ * cdef bam_plbuf_t * buf
+ * buf = <bam_plbuf_t*>data
+ * bam_plbuf_push(b, buf) # <<<<<<<<<<<<<<
+ * return 0
+ *
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
- if (__pyx_t_1) {
- free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
- goto __pyx_L6;
- }
- __pyx_L6:;
+ bam_plbuf_push(__pyx_v_b, __pyx_v_buf);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":285
- * if self.fastafile != NULL: self.close()
- * if self._filename != NULL: free(self._filename)
- * self._filename = strdup(filename) # <<<<<<<<<<<<<<
- * self.fastafile = fai_load( filename )
+ /* "csamtools.pyx":302
+ * buf = <bam_plbuf_t*>data
+ * bam_plbuf_push(b, buf)
+ * return 0 # <<<<<<<<<<<<<<
*
+ * class StderrStore():
*/
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = strdup(__pyx_v_filename);
+ __pyx_r = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":286
- * if self._filename != NULL: free(self._filename)
- * self._filename = strdup(filename)
- * self.fastafile = fai_load( filename ) # <<<<<<<<<<<<<<
- *
- * if self.fastafile == NULL:
- */
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = fai_load(__pyx_v_filename);
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":288
- * self.fastafile = fai_load( filename )
- *
- * if self.fastafile == NULL: # <<<<<<<<<<<<<<
- * raise IOError("could not open file `%s`" % filename )
- *
- */
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
- if (__pyx_t_1) {
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___init__)};
+static PyObject *__pyx_pw_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_11StderrStore___init__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":289
- *
- * if self.fastafile == NULL:
- * raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
- *
- * def close( self ):
+/* "csamtools.pyx":308
+ * stderr is captured.
+ * '''
+ * def __init__(self): # <<<<<<<<<<<<<<
+ * return
+ * self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_4), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
- }
- __pyx_L7:;
+static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 308);
+
+ /* "csamtools.pyx":309
+ * '''
+ * def __init__(self):
+ * return # <<<<<<<<<<<<<<
+ * self.stderr_h, self.stderr_f = tempfile.mkstemp()
+ * self.stderr_save = Outs( sys.stderr.fileno() )
+ */
+ __Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Fastafile._open");
- __pyx_r = NULL;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":291
- * raise IOError("could not open file `%s`" % filename )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_2readAndRelease[] = "StderrStore.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_2readAndRelease)};
+static PyObject *__pyx_pw_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_11StderrStore_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":314
+ * self.stderr_save.setfd( self.stderr_h )
*
- * def close( self ): # <<<<<<<<<<<<<<
- * if self.fastafile != NULL:
- * fai_destroy( self.fastafile )
+ * def readAndRelease( self ): # <<<<<<<<<<<<<<
+ * return []
+ * self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_close[] = "Fastafile.close(self)";
-static PyObject *__pyx_pf_9csamtools_9Fastafile_close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- int __pyx_t_1;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close");
- __Pyx_TraceCall("close", __pyx_f[0], 291);
+ __Pyx_RefNannySetupContext("readAndRelease", 0);
+ __Pyx_TraceCall("readAndRelease", __pyx_f[0], 314);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":292
+ /* "csamtools.pyx":315
*
- * def close( self ):
- * if self.fastafile != NULL: # <<<<<<<<<<<<<<
- * fai_destroy( self.fastafile )
- * self.fastafile = NULL
+ * def readAndRelease( self ):
+ * return [] # <<<<<<<<<<<<<<
+ * self.stderr_save.restore()
+ * lines = []
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
- if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":293
- * def close( self ):
- * if self.fastafile != NULL:
- * fai_destroy( self.fastafile ) # <<<<<<<<<<<<<<
- * self.fastafile = NULL
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.StderrStore.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_4release[] = "StderrStore.release(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_4release)};
+static PyObject *__pyx_pw_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("release (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_11StderrStore_4release(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":323
+ * return lines
*
+ * def release(self): # <<<<<<<<<<<<<<
+ * return
+ * self.stderr_save.restore()
*/
- fai_destroy(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":294
- * if self.fastafile != NULL:
- * fai_destroy( self.fastafile )
- * self.fastafile = NULL # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("release", 0);
+ __Pyx_TraceCall("release", __pyx_f[0], 323);
+
+ /* "csamtools.pyx":324
*
- * def __dealloc__(self):
+ * def release(self):
+ * return # <<<<<<<<<<<<<<
+ * self.stderr_save.restore()
+ * if os.path.exists(self.stderr_f):
*/
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":296
- * self.fastafile = NULL
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_6__del__[] = "StderrStore.__del__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_7__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_7__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_6__del__)};
+static PyObject *__pyx_pw_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_11StderrStore_6__del__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":329
+ * os.remove( self.stderr_f )
+ *
+ * def __del__(self): # <<<<<<<<<<<<<<
+ * self.release()
*
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * self.close()
- * if self._filename != NULL: free(self._filename)
*/
-static void __pyx_pf_9csamtools_9Fastafile___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_9Fastafile___dealloc__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 296);
+ __Pyx_RefNannySetupContext("__del__", 0);
+ __Pyx_TraceCall("__del__", __pyx_f[0], 329);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":297
+ /* "csamtools.pyx":330
*
- * def __dealloc__(self):
- * self.close() # <<<<<<<<<<<<<<
- * if self._filename != NULL: free(self._filename)
+ * def __del__(self):
+ * self.release() # <<<<<<<<<<<<<<
*
+ * class StderrStoreWindows():
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__release); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":298
- * def __dealloc__(self):
- * self.close()
- * if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
- *
- * property filename:
- */
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
- if (__pyx_t_3) {
- free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
- goto __pyx_L5;
- }
- __pyx_L5:;
-
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.__dealloc__");
+ __Pyx_AddTraceback("csamtools.StderrStore.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":302
- * property filename:
- * '''number of :term:`filename` associated with this object.'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self._filename
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_9csamtools_18StderrStoreWindows_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows___init__)};
+static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_18StderrStoreWindows___init__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":334
+ * class StderrStoreWindows():
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass # <<<<<<<<<<<<<<
+ * def readAndRelease(self): return []
+ * def release(self): pass
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 302);
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 334);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":303
- * '''number of :term:`filename` associated with this object.'''
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * return self._filename
- *
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":304
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self._filename # <<<<<<<<<<<<<<
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows_2readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_2readAndRelease)};
+static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":335
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass
+ * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
+ * def release(self): pass
*
- * def fetch( self,
*/
+
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("readAndRelease", 0);
+ __Pyx_TraceCall("readAndRelease", __pyx_f[0], 335);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.filename.__get__");
+ __Pyx_AddTraceback("csamtools.StderrStoreWindows.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":306
- * return self._filename
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_9Fastafile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n \n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing. \n \n The region is specified by :term:`reference`, *start* and *end*. \n \n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* is given and *start* is None, the sequence from the \n first base is returned. Similarly, if *end* is None, the sequence \n until the last base is returned.\n \n Alternatively, a samtools :term:`region` string can be supplied.\n ";
-static PyObject *__pyx_pf_9csamtools_9Fastafile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_reference = 0;
- PyObject *__pyx_v_start = 0;
- PyObject *__pyx_v_end = 0;
- PyObject *__pyx_v_region = 0;
- int __pyx_v_length;
- char *__pyx_v_seq;
- PyObject *__pyx_v_py_seq;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows_4release[] = "StderrStoreWindows.release(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_9csamtools_18StderrStoreWindows_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_4release)};
+static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("release (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_18StderrStoreWindows_4release(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":336
+ * def __init__(self): pass
+ * def readAndRelease(self): return []
+ * def release(self): pass # <<<<<<<<<<<<<<
+ *
+ * if platform.system()=='Windows':
+ */
+
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch");
- __Pyx_TraceCall("fetch", __pyx_f[0], 306);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[4] = {0,0,0,0};
+ __Pyx_RefNannySetupContext("release", 0);
+ __Pyx_TraceCall("release", __pyx_f[0], 336);
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":307
+/* Python wrapper */
+static int __pyx_pw_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile___cinit__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":387
+ * '''
*
- * def fetch( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
+ * def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
+ * self.fastafile = NULL
+ * self._filename = NULL
*/
- values[0] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":308
- * def fetch( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None):
- */
- values[1] = ((PyObject *)Py_None);
+static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 387);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":309
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None):
+ /* "csamtools.pyx":388
*
+ * def __cinit__(self, *args, **kwargs ):
+ * self.fastafile = NULL # <<<<<<<<<<<<<<
+ * self._filename = NULL
+ * self._open( *args, **kwargs )
*/
- values[2] = ((PyObject *)Py_None);
+ __pyx_v_self->fastafile = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":310
- * start = None,
- * end = None,
- * region = None): # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":389
+ * def __cinit__(self, *args, **kwargs ):
+ * self.fastafile = NULL
+ * self._filename = NULL # <<<<<<<<<<<<<<
+ * self._open( *args, **kwargs )
*
- * '''*(reference = None, start = None, end = None, region = None)*
*/
- values[3] = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (value) { values[0] = value; kw_args--; }
- }
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
- if (value) { values[3] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_reference = values[0];
- __pyx_v_start = values[1];
- __pyx_v_end = values[2];
- __pyx_v_region = values[3];
- } else {
+ __pyx_v_self->_filename = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":307
+ /* "csamtools.pyx":390
+ * self.fastafile = NULL
+ * self._filename = NULL
+ * self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
*
- * def fetch( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
+ * def _isOpen( self ):
*/
- __pyx_v_reference = ((PyObject *)Py_None);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":308
- * def fetch( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None):
- */
- __pyx_v_start = ((PyObject *)Py_None);
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.Fastafile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":309
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None):
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_2_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pw_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile_2_isOpen(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":392
+ * self._open( *args, **kwargs )
*
+ * def _isOpen( self ): # <<<<<<<<<<<<<<
+ * '''return true if samfile has been opened.'''
+ * return self.fastafile != NULL
*/
- __pyx_v_end = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":310
- * start = None,
- * end = None,
- * region = None): # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_isOpen", 0);
+ __Pyx_TraceCall("_isOpen", __pyx_f[0], 392);
+
+ /* "csamtools.pyx":394
+ * def _isOpen( self ):
+ * '''return true if samfile has been opened.'''
+ * return self.fastafile != NULL # <<<<<<<<<<<<<<
*
- * '''*(reference = None, start = None, end = None, region = None)*
+ * def __len__(self):
*/
- __pyx_v_region = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: __pyx_v_region = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_end = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: __pyx_v_start = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Fastafile.fetch");
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.Fastafile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __Pyx_INCREF(__pyx_v_start);
- __Pyx_INCREF(__pyx_v_end);
- __Pyx_INCREF(__pyx_v_region);
- __pyx_v_py_seq = Py_None; __Pyx_INCREF(Py_None);
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":327
- * '''
- *
- * if not self._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
+/* Python wrapper */
+static Py_ssize_t __pyx_pw_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self); /*proto*/
+static Py_ssize_t __pyx_pw_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self) {
+ Py_ssize_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile_4__len__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":396
+ * return self.fastafile != NULL
*
+ * def __len__(self): # <<<<<<<<<<<<<<
+ * if self.fastafile == NULL:
+ * raise ValueError( "calling len() on closed file" )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":328
+static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+ Py_ssize_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__len__", 0);
+ __Pyx_TraceCall("__len__", __pyx_f[0], 396);
+
+ /* "csamtools.pyx":397
*
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * def __len__(self):
+ * if self.fastafile == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "calling len() on closed file" )
*
- * cdef int length
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":398
+ * def __len__(self):
+ * if self.fastafile == NULL:
+ * raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * return faidx_fetch_nseq(self.fastafile)
+ */
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":333
- * cdef char * seq
+ /* "csamtools.pyx":400
+ * raise ValueError( "calling len() on closed file" )
*
- * if not region: # <<<<<<<<<<<<<<
- * if reference is None: raise ValueError( 'no sequence/region supplied.' )
- * if start is None: start = 0
- */
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":334
+ * return faidx_fetch_nseq(self.fastafile) # <<<<<<<<<<<<<<
*
- * if not region:
- * if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
- * if start is None: start = 0
- * if end is None: end = max_pos -1
+ * def _open( self,
*/
- __pyx_t_3 = (__pyx_v_reference == Py_None);
- if (__pyx_t_3) {
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
- }
- __pyx_L8:;
+ __pyx_r = faidx_fetch_nseq(__pyx_v_self->fastafile);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":335
- * if not region:
- * if reference is None: raise ValueError( 'no sequence/region supplied.' )
- * if start is None: start = 0 # <<<<<<<<<<<<<<
- * if end is None: end = max_pos -1
- *
- */
- __pyx_t_3 = (__pyx_v_start == Py_None);
- if (__pyx_t_3) {
- __Pyx_INCREF(__pyx_int_0);
- __Pyx_DECREF(__pyx_v_start);
- __pyx_v_start = __pyx_int_0;
- goto __pyx_L9;
- }
- __pyx_L9:;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Fastafile.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":336
- * if reference is None: raise ValueError( 'no sequence/region supplied.' )
- * if start is None: start = 0
- * if end is None: end = max_pos -1 # <<<<<<<<<<<<<<
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_6_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
+static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_open (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile_6_open(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), ((PyObject *)__pyx_v_filename));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":402
+ * return faidx_fetch_nseq(self.fastafile)
*
- * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
+ * def _open( self, # <<<<<<<<<<<<<<
+ * filename ):
+ * '''open an indexed fasta file.
*/
- __pyx_t_3 = (__pyx_v_end == Py_None);
- if (__pyx_t_3) {
- __pyx_t_2 = PyInt_FromLong((__pyx_v_9csamtools_max_pos - 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_end);
- __pyx_v_end = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L10;
- }
- __pyx_L10:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":338
- * if end is None: end = max_pos -1
+static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ char *__pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_open", 0);
+ __Pyx_TraceCall("_open", __pyx_f[0], 402);
+ __Pyx_INCREF(__pyx_v_filename);
+
+ /* "csamtools.pyx":410
*
- * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) # <<<<<<<<<<<<<<
- * if start == end: return ""
- * # valid ranges are from 0 to 2^29-1
+ * # close a previously opened file
+ * if self.fastafile != NULL: self.close() # <<<<<<<<<<<<<<
+ * if self._filename != NULL: free(self._filename)
+ * filename = _my_encodeFilename(filename)
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
+ if (__pyx_t_1) {
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_3) {
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_start);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start);
- __Pyx_GIVEREF(__pyx_v_start);
- __Pyx_INCREF(__pyx_v_end);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_end);
- __Pyx_GIVEREF(__pyx_v_end);
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_7), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
- }
- __pyx_L11:;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":339
- *
- * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
- * if start == end: return "" # <<<<<<<<<<<<<<
- * # valid ranges are from 0 to 2^29-1
- * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
+ /* "csamtools.pyx":411
+ * # close a previously opened file
+ * if self.fastafile != NULL: self.close()
+ * if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
+ * filename = _my_encodeFilename(filename)
+ * self._filename = strdup(filename)
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_3) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_8));
- __pyx_r = ((PyObject *)__pyx_kp_s_8);
- goto __pyx_L0;
- goto __pyx_L12;
- }
- __pyx_L12:;
+ __pyx_t_1 = (__pyx_v_self->_filename != NULL);
+ if (__pyx_t_1) {
+ free(__pyx_v_self->_filename);
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":341
- * if start == end: return ""
- * # valid ranges are from 0 to 2^29-1
- * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
- * if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end )
- * # note: faidx_fetch_seq has a bug such that out-of-range access
+ /* "csamtools.pyx":412
+ * if self.fastafile != NULL: self.close()
+ * if self._filename != NULL: free(self._filename)
+ * filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<<
+ * self._filename = strdup(filename)
+ * self.fastafile = fai_load( filename )
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
- __Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- }
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L13;
- }
- __pyx_L13:;
+ __pyx_t_3 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_v_filename);
+ __pyx_v_filename = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":342
- * # valid ranges are from 0 to 2^29-1
- * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
- * if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
- * # note: faidx_fetch_seq has a bug such that out-of-range access
- * # always returns the last residue. Hence do not use faidx_fetch_seq,
+ /* "csamtools.pyx":413
+ * if self._filename != NULL: free(self._filename)
+ * filename = _my_encodeFilename(filename)
+ * self._filename = strdup(filename) # <<<<<<<<<<<<<<
+ * self.fastafile = fai_load( filename )
+ *
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
- __Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- }
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_10), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
- }
- __pyx_L14:;
+ __pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_filename = strdup(__pyx_t_4);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":351
- * # end-1,
- * # &length)
- * region = "%s:%i-%i" % (reference, start+1, end) # <<<<<<<<<<<<<<
- * seq = fai_fetch( self.fastafile,
- * region,
+ /* "csamtools.pyx":414
+ * filename = _my_encodeFilename(filename)
+ * self._filename = strdup(filename)
+ * self.fastafile = fai_load( filename ) # <<<<<<<<<<<<<<
+ *
+ * if self.fastafile == NULL:
*/
- __pyx_t_1 = PyNumber_Add(__pyx_v_start, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
- __Pyx_GIVEREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_end);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end);
- __Pyx_GIVEREF(__pyx_v_end);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_11), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_v_region);
- __pyx_v_region = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fastafile = fai_load(__pyx_t_4);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":353
- * region = "%s:%i-%i" % (reference, start+1, end)
- * seq = fai_fetch( self.fastafile,
- * region, # <<<<<<<<<<<<<<
- * &length )
- * else:
+ /* "csamtools.pyx":416
+ * self.fastafile = fai_load( filename )
+ *
+ * if self.fastafile == NULL: # <<<<<<<<<<<<<<
+ * raise IOError("could not open file `%s`" % filename )
+ *
*/
- __pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":354
- * seq = fai_fetch( self.fastafile,
- * region,
- * &length ) # <<<<<<<<<<<<<<
- * else:
- * # samtools adds a '\0' at the end
+ /* "csamtools.pyx":417
+ *
+ * if self.fastafile == NULL:
+ * raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
+ *
+ * def close( self ):
*/
- __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
- goto __pyx_L7;
+ __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- /*else*/ {
+ __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":357
- * else:
- * # samtools adds a '\0' at the end
- * seq = fai_fetch( self.fastafile, region, &length ) # <<<<<<<<<<<<<<
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.Fastafile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_filename);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_8close[] = "Fastafile.close(self)";
+static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("close (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile_8close(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":419
+ * raise IOError("could not open file `%s`" % filename )
*
- * # copy to python
+ * def close( self ): # <<<<<<<<<<<<<<
+ * if self.fastafile != NULL:
+ * fai_destroy( self.fastafile )
*/
- __pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
- }
- __pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":360
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_TraceCall("close", __pyx_f[0], 419);
+
+ /* "csamtools.pyx":420
*
- * # copy to python
- * if seq == NULL: # <<<<<<<<<<<<<<
- * return ""
- * else:
+ * def close( self ):
+ * if self.fastafile != NULL: # <<<<<<<<<<<<<<
+ * fai_destroy( self.fastafile )
+ * self.fastafile = NULL
*/
- __pyx_t_3 = (__pyx_v_seq == NULL);
- if (__pyx_t_3) {
+ __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":361
- * # copy to python
- * if seq == NULL:
- * return "" # <<<<<<<<<<<<<<
- * else:
- * try:
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_8));
- __pyx_r = ((PyObject *)__pyx_kp_s_8);
- goto __pyx_L0;
- goto __pyx_L15;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":363
- * return ""
- * else:
- * try: # <<<<<<<<<<<<<<
- * py_seq = PyString_FromStringAndSize(seq, length)
- * finally:
- */
- /*try:*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":364
- * else:
- * try:
- * py_seq = PyString_FromStringAndSize(seq, length) # <<<<<<<<<<<<<<
- * finally:
- * free(seq)
- */
- __pyx_t_1 = PyString_FromStringAndSize(__pyx_v_seq, __pyx_v_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L17;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_v_py_seq);
- __pyx_v_py_seq = __pyx_t_1;
- __pyx_t_1 = 0;
- }
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":366
- * py_seq = PyString_FromStringAndSize(seq, length)
- * finally:
- * free(seq) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":421
+ * def close( self ):
+ * if self.fastafile != NULL:
+ * fai_destroy( self.fastafile ) # <<<<<<<<<<<<<<
+ * self.fastafile = NULL
*
- * return py_seq
*/
- /*finally:*/ {
- int __pyx_why;
- PyObject *__pyx_exc_type, *__pyx_exc_value, *__pyx_exc_tb;
- int __pyx_exc_lineno;
- __pyx_exc_type = 0; __pyx_exc_value = 0; __pyx_exc_tb = 0; __pyx_exc_lineno = 0;
- __pyx_why = 0; goto __pyx_L18;
- __pyx_L17: {
- __pyx_why = 4;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_ErrFetch(&__pyx_exc_type, &__pyx_exc_value, &__pyx_exc_tb);
- __pyx_exc_lineno = __pyx_lineno;
- goto __pyx_L18;
- }
- __pyx_L18:;
- free(__pyx_v_seq);
- switch (__pyx_why) {
- case 4: {
- __Pyx_ErrRestore(__pyx_exc_type, __pyx_exc_value, __pyx_exc_tb);
- __pyx_lineno = __pyx_exc_lineno;
- __pyx_exc_type = 0;
- __pyx_exc_value = 0;
- __pyx_exc_tb = 0;
- goto __pyx_L1_error;
- }
- }
- }
- }
- __pyx_L15:;
+ fai_destroy(__pyx_v_self->fastafile);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":368
- * free(seq)
- *
- * return py_seq # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":422
+ * if self.fastafile != NULL:
+ * fai_destroy( self.fastafile )
+ * self.fastafile = NULL # <<<<<<<<<<<<<<
*
- * cdef char * _fetch( self, char * reference, int start, int end, int * length ):
+ * def __dealloc__(self):
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_py_seq);
- __pyx_r = __pyx_v_py_seq;
- goto __pyx_L0;
+ __pyx_v_self->fastafile = NULL;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.fetch");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_py_seq);
- __Pyx_DECREF(__pyx_v_start);
- __Pyx_DECREF(__pyx_v_end);
- __Pyx_DECREF(__pyx_v_region);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":370
- * return py_seq
- *
- * cdef char * _fetch( self, char * reference, int start, int end, int * length ): # <<<<<<<<<<<<<<
- * '''fetch sequence for reference, start and end'''
+/* Python wrapper */
+static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_9Fastafile_10__dealloc__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "csamtools.pyx":424
+ * self.fastafile = NULL
*
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * self.close()
+ * if self._filename != NULL: free(self._filename)
*/
-static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, char *__pyx_v_reference, int __pyx_v_start, int __pyx_v_end, int *__pyx_v_length) {
- char *__pyx_r;
+static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_fetch");
- __Pyx_TraceCall("_fetch", __pyx_f[0], 370);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 424);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":377
- * start,
- * end-1,
- * length ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":425
+ *
+ * def __dealloc__(self):
+ * self.close() # <<<<<<<<<<<<<<
+ * if self._filename != NULL: free(self._filename)
*
- * #------------------------------------------------------------------------
*/
- __pyx_r = faidx_fetch_seq(__pyx_v_self->fastafile, __pyx_v_reference, __pyx_v_start, (__pyx_v_end - 1), __pyx_v_length);
- goto __pyx_L0;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = 0;
+ /* "csamtools.pyx":426
+ * def __dealloc__(self):
+ * self.close()
+ * if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
+ *
+ * property filename:
+ */
+ __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ if (__pyx_t_3) {
+ free(__pyx_v_self->_filename);
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Fastafile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile_8filename___get__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":382
- * #------------------------------------------------------------------------
- * #------------------------------------------------------------------------
- * cdef int count_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
- * '''callback for bam_fetch - count number of reads.
- * '''
+/* "csamtools.pyx":430
+ * property filename:
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return self._filename
*/
-static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
- int *__pyx_v_counter;
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count_callback");
- __Pyx_TraceCall("count_callback", __pyx_f[0], 382);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 430);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":385
- * '''callback for bam_fetch - count number of reads.
- * '''
- * cdef int* counter = (<int*>f) # <<<<<<<<<<<<<<
- * counter[0] += 1;
+ /* "csamtools.pyx":431
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self._filename
*
*/
- __pyx_v_counter = ((int *)__pyx_v_f);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_11), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":386
- * '''
- * cdef int* counter = (<int*>f)
- * counter[0] += 1; # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":432
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return self._filename # <<<<<<<<<<<<<<
*
- * ctypedef struct MateData:
+ * def fetch( self,
*/
- (__pyx_v_counter[0]) += 1;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- __pyx_r = 0;
- __Pyx_TraceReturn(Py_None);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Fastafile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":396
- * #------------------------------------------------------------------------
- * #------------------------------------------------------------------------
- * cdef int mate_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
- * '''callback for bam_fetch = filter mate
- * '''
- */
-
-static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
- __pyx_t_9csamtools_MateData *__pyx_v_d;
- int __pyx_r;
- int __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate_callback");
- __Pyx_TraceCall("mate_callback", __pyx_f[0], 396);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":399
- * '''callback for bam_fetch = filter mate
- * '''
- * cdef MateData * d = (<MateData*>f) # <<<<<<<<<<<<<<
- * # printf("mate = %p, name1 = %s, name2=%s\t%i\t%i\t%i\n",
- * # d.mate, d.name, bam1_qname(alignment),
- */
- __pyx_v_d = ((__pyx_t_9csamtools_MateData *)__pyx_v_f);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_12fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* is given and *start* is None, the sequence from the\n first base is returned. Similarly, if *end* is None, the sequence\n until the last base is returned.\n\n Alternatively, a samtools :term:`region` string can be supplied.\n ";
+static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_reference = 0;
+ PyObject *__pyx_v_start = 0;
+ PyObject *__pyx_v_end = 0;
+ PyObject *__pyx_v_region = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ {
+ PyObject* values[4] = {0,0,0,0};
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":404
- * # d.flag, alignment.core.flag, alignment.core.flag & d.flag)
+ /* "csamtools.pyx":435
*
- * if d.mate == NULL: # <<<<<<<<<<<<<<
- * # could be sped up by comparing the lengths of query strings first
- * # using l_qname
+ * def fetch( self,
+ * reference = None, # <<<<<<<<<<<<<<
+ * start = None,
+ * end = None,
*/
- __pyx_t_1 = (__pyx_v_d->mate == NULL);
- if (__pyx_t_1) {
+ values[0] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":410
- * # also, make sure that we get the other read by comparing
- * # the flags
- * if alignment.core.flag & d.flag != 0 and \ # <<<<<<<<<<<<<<
- * strcmp( bam1_qname( alignment ), d.name ) == 0:
- * d.mate = bam_dup1( alignment )
+ /* "csamtools.pyx":436
+ * def fetch( self,
+ * reference = None,
+ * start = None, # <<<<<<<<<<<<<<
+ * end = None,
+ * region = None):
*/
- __pyx_t_1 = ((__pyx_v_alignment->core.flag & __pyx_v_d->flag) != 0);
- if (__pyx_t_1) {
+ values[1] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":411
- * # the flags
- * if alignment.core.flag & d.flag != 0 and \
- * strcmp( bam1_qname( alignment ), d.name ) == 0: # <<<<<<<<<<<<<<
- * d.mate = bam_dup1( alignment )
+ /* "csamtools.pyx":437
+ * reference = None,
+ * start = None,
+ * end = None, # <<<<<<<<<<<<<<
+ * region = None):
*
*/
- __pyx_t_2 = (strcmp(bam1_qname(__pyx_v_alignment), __pyx_v_d->name) == 0);
- __pyx_t_3 = __pyx_t_2;
- } else {
- __pyx_t_3 = __pyx_t_1;
- }
- if (__pyx_t_3) {
+ values[2] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":412
- * if alignment.core.flag & d.flag != 0 and \
- * strcmp( bam1_qname( alignment ), d.name ) == 0:
- * d.mate = bam_dup1( alignment ) # <<<<<<<<<<<<<<
- *
+ /* "csamtools.pyx":438
+ * start = None,
+ * end = None,
+ * region = None): # <<<<<<<<<<<<<<
*
+ * '''*(reference = None, start = None, end = None, region = None)*
*/
- __pyx_v_d->mate = bam_dup1(__pyx_v_alignment);
- goto __pyx_L4;
+ values[3] = ((PyObject *)Py_None);
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
+ if (value) { values[0] = value; kw_args--; }
+ }
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
}
- __pyx_L4:;
- goto __pyx_L3;
+ __pyx_v_reference = values[0];
+ __pyx_v_start = values[1];
+ __pyx_v_end = values[2];
+ __pyx_v_region = values[3];
}
- __pyx_L3:;
-
- __pyx_r = 0;
- __Pyx_TraceReturn(Py_None);
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_9Fastafile_12fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":455
- * '''
+/* "csamtools.pyx":434
+ * return self._filename
*
- * def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
- * self.samfile = NULL
- * self._filename = NULL
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
*/
-static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
+ int __pyx_v_length;
+ char *__pyx_v_seq;
+ PyObject *__pyx_v_py_seq = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 455);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":456
- *
- * def __cinit__(self, *args, **kwargs ):
- * self.samfile = NULL # <<<<<<<<<<<<<<
- * self._filename = NULL
- * self.isbam = False
- */
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":457
- * def __cinit__(self, *args, **kwargs ):
- * self.samfile = NULL
- * self._filename = NULL # <<<<<<<<<<<<<<
- * self.isbam = False
- * self._open( *args, **kwargs )
- */
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = NULL;
+ __Pyx_RefNannySetupContext("fetch", 0);
+ __Pyx_TraceCall("fetch", __pyx_f[0], 434);
+ __Pyx_INCREF(__pyx_v_start);
+ __Pyx_INCREF(__pyx_v_end);
+ __Pyx_INCREF(__pyx_v_region);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":458
- * self.samfile = NULL
- * self._filename = NULL
- * self.isbam = False # <<<<<<<<<<<<<<
- * self._open( *args, **kwargs )
+ /* "csamtools.pyx":455
+ * '''
*
- */
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":459
- * self._filename = NULL
- * self.isbam = False
- * self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
+ * if not self._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
*
- * # allocate memory for iterator
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":462
+ /* "csamtools.pyx":456
*
- * # allocate memory for iterator
- * self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
- * def _isOpen( self ):
+ * cdef int length
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Samfile.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_args);
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_12), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":464
- * self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
+ /* "csamtools.pyx":461
+ * cdef char * seq
*
- * def _isOpen( self ): # <<<<<<<<<<<<<<
- * '''return true if samfile has been opened.'''
- * return self.samfile != NULL
+ * if not region: # <<<<<<<<<<<<<<
+ * if reference is None: raise ValueError( 'no sequence/region supplied.' )
+ * if start is None: start = 0
*/
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
-static PyObject *__pyx_pf_9csamtools_7Samfile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile__isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pf_9csamtools_7Samfile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen");
- __Pyx_TraceCall("_isOpen", __pyx_f[0], 464);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":466
- * def _isOpen( self ):
- * '''return true if samfile has been opened.'''
- * return self.samfile != NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":462
*
- * def _hasIndex( self ):
+ * if not region:
+ * if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
+ * if start is None: start = 0
+ * if end is None: end = max_pos -1
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Samfile._isOpen");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_3 = (__pyx_v_reference == Py_None);
+ if (__pyx_t_3) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_14), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":468
- * return self.samfile != NULL
+ /* "csamtools.pyx":463
+ * if not region:
+ * if reference is None: raise ValueError( 'no sequence/region supplied.' )
+ * if start is None: start = 0 # <<<<<<<<<<<<<<
+ * if end is None: end = max_pos -1
*
- * def _hasIndex( self ): # <<<<<<<<<<<<<<
- * '''return true if samfile has an existing (and opened) index.'''
- * return self.index != NULL
*/
+ __pyx_t_3 = (__pyx_v_start == Py_None);
+ if (__pyx_t_3) {
+ __Pyx_INCREF(__pyx_int_0);
+ __Pyx_DECREF(__pyx_v_start);
+ __pyx_v_start = __pyx_int_0;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
-static PyObject *__pyx_pf_9csamtools_7Samfile__hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile__hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
-static PyObject *__pyx_pf_9csamtools_7Samfile__hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_hasIndex");
- __Pyx_TraceCall("_hasIndex", __pyx_f[0], 468);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":470
- * def _hasIndex( self ):
- * '''return true if samfile has an existing (and opened) index.'''
- * return self.index != NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":464
+ * if reference is None: raise ValueError( 'no sequence/region supplied.' )
+ * if start is None: start = 0
+ * if end is None: end = max_pos -1 # <<<<<<<<<<<<<<
*
- * def _open( self,
+ * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Samfile._hasIndex");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_3 = (__pyx_v_end == Py_None);
+ if (__pyx_t_3) {
+ __pyx_t_2 = PyInt_FromLong((__pyx_v_9csamtools_max_pos - 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_v_end);
+ __pyx_v_end = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":472
- * return self.index != NULL
+ /* "csamtools.pyx":466
+ * if end is None: end = max_pos -1
*
- * def _open( self, # <<<<<<<<<<<<<<
- * char * filename,
- * mode = None,
+ * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) # <<<<<<<<<<<<<<
+ * if start == end: return b""
+ * # valid ranges are from 0 to 2^29-1
*/
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_3) {
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_start);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start);
+ __Pyx_GIVEREF(__pyx_v_start);
+ __Pyx_INCREF(__pyx_v_end);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_end);
+ __Pyx_GIVEREF(__pyx_v_end);
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_15), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
-static PyObject *__pyx_pf_9csamtools_7Samfile__open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile__open[] = "Samfile._open(self, char *filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile__open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- char *__pyx_v_filename;
- PyObject *__pyx_v_mode = 0;
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_template = 0;
- PyObject *__pyx_v_referencenames = 0;
- PyObject *__pyx_v_referencelengths = 0;
- PyObject *__pyx_v_text = 0;
- PyObject *__pyx_v_header = 0;
- PyObject *__pyx_v_port = 0;
- PyObject *__pyx_v_msg;
- bam_header_t *__pyx_v_header_to_write;
- char *__pyx_v_ctext;
- PyObject *__pyx_v_n;
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_name;
- PyObject *__pyx_v_store;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- int __pyx_t_6;
- int __pyx_t_7;
- int __pyx_t_8;
- Py_ssize_t __pyx_t_9;
- Py_ssize_t __pyx_t_10;
- size_t __pyx_t_11;
- int32_t __pyx_t_12;
- long __pyx_t_13;
- uint32_t __pyx_t_14;
- char *__pyx_t_15;
- int __pyx_t_16;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open");
- __Pyx_TraceCall("_open", __pyx_f[0], 472);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[8] = {0,0,0,0,0,0,0,0};
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":474
- * def _open( self,
- * char * filename,
- * mode = None, # <<<<<<<<<<<<<<
- * Samfile template = None,
- * referencenames = None,
- */
- values[1] = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":475
- * char * filename,
- * mode = None,
- * Samfile template = None, # <<<<<<<<<<<<<<
- * referencenames = None,
- * referencelengths = None,
+ /* "csamtools.pyx":467
+ *
+ * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
+ * if start == end: return b"" # <<<<<<<<<<<<<<
+ * # valid ranges are from 0 to 2^29-1
+ * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
*/
- values[2] = (PyObject *)((struct __pyx_obj_9csamtools_Samfile *)Py_None);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_3) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
+ __pyx_r = ((PyObject *)__pyx_kp_b_16);
+ goto __pyx_L0;
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":476
- * mode = None,
- * Samfile template = None,
- * referencenames = None, # <<<<<<<<<<<<<<
- * referencelengths = None,
- * text = None,
+ /* "csamtools.pyx":469
+ * if start == end: return b""
+ * # valid ranges are from 0 to 2^29-1
+ * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
+ * if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end )
+ * # note: faidx_fetch_seq has a bug such that out-of-range access
*/
- values[3] = ((PyObject *)Py_None);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
+ __Pyx_DECREF(__pyx_t_1);
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ }
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L10;
+ }
+ __pyx_L10:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":477
- * Samfile template = None,
- * referencenames = None,
- * referencelengths = None, # <<<<<<<<<<<<<<
- * text = None,
- * header = None,
+ /* "csamtools.pyx":470
+ * # valid ranges are from 0 to 2^29-1
+ * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
+ * if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
+ * # note: faidx_fetch_seq has a bug such that out-of-range access
+ * # always returns the last residue. Hence do not use faidx_fetch_seq,
*/
- values[4] = ((PyObject *)Py_None);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
+ __Pyx_DECREF(__pyx_t_1);
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ }
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L11;
+ }
+ __pyx_L11:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":478
- * referencenames = None,
- * referencelengths = None,
- * text = None, # <<<<<<<<<<<<<<
- * header = None,
- * port = None,
+ /* "csamtools.pyx":479
+ * # end-1,
+ * # &length)
+ * region = "%s:%i-%i" % (reference, start+1, end) # <<<<<<<<<<<<<<
+ * if PY_MAJOR_VERSION >= 3:
+ * region = region.encode('ascii')
*/
- values[5] = ((PyObject *)Py_None);
+ __pyx_t_1 = PyNumber_Add(__pyx_v_start, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_reference);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
+ __Pyx_GIVEREF(__pyx_v_reference);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_end);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end);
+ __Pyx_GIVEREF(__pyx_v_end);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_v_region);
+ __pyx_v_region = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":479
- * referencelengths = None,
- * text = None,
- * header = None, # <<<<<<<<<<<<<<
- * port = None,
- * ):
+ /* "csamtools.pyx":480
+ * # &length)
+ * region = "%s:%i-%i" % (reference, start+1, end)
+ * if PY_MAJOR_VERSION >= 3: # <<<<<<<<<<<<<<
+ * region = region.encode('ascii')
+ * seq = fai_fetch( self.fastafile,
*/
- values[6] = ((PyObject *)Py_None);
+ __pyx_t_3 = (PY_MAJOR_VERSION >= 3);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":480
- * text = None,
- * header = None,
- * port = None, # <<<<<<<<<<<<<<
- * ):
- * '''open a sam/bam file.
+ /* "csamtools.pyx":481
+ * region = "%s:%i-%i" % (reference, start+1, end)
+ * if PY_MAJOR_VERSION >= 3:
+ * region = region.encode('ascii') # <<<<<<<<<<<<<<
+ * seq = fai_fetch( self.fastafile,
+ * region,
*/
- values[7] = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 8: values[7] = PyTuple_GET_ITEM(__pyx_args, 7);
- case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
- case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
- case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__mode);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__template);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__referencenames);
- if (value) { values[3] = value; kw_args--; }
- }
- case 4:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__referencelengths);
- if (value) { values[4] = value; kw_args--; }
- }
- case 5:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__text);
- if (value) { values[5] = value; kw_args--; }
- }
- case 6:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header);
- if (value) { values[6] = value; kw_args--; }
- }
- case 7:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__port);
- if (value) { values[7] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_region, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_20), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_v_region);
+ __pyx_v_region = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L12;
}
- __pyx_v_filename = PyBytes_AsString(values[0]); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_mode = values[1];
- __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)values[2]);
- __pyx_v_referencenames = values[3];
- __pyx_v_referencelengths = values[4];
- __pyx_v_text = values[5];
- __pyx_v_header = values[6];
- __pyx_v_port = values[7];
- } else {
+ __pyx_L12:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":474
- * def _open( self,
- * char * filename,
- * mode = None, # <<<<<<<<<<<<<<
- * Samfile template = None,
- * referencenames = None,
+ /* "csamtools.pyx":483
+ * region = region.encode('ascii')
+ * seq = fai_fetch( self.fastafile,
+ * region, # <<<<<<<<<<<<<<
+ * &length )
+ * else:
*/
- __pyx_v_mode = ((PyObject *)Py_None);
+ __pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":475
- * char * filename,
- * mode = None,
- * Samfile template = None, # <<<<<<<<<<<<<<
- * referencenames = None,
- * referencelengths = None,
+ /* "csamtools.pyx":484
+ * seq = fai_fetch( self.fastafile,
+ * region,
+ * &length ) # <<<<<<<<<<<<<<
+ * else:
+ * # samtools adds a '\0' at the end
*/
- __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)Py_None);
+ __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
+ goto __pyx_L4;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":476
- * mode = None,
- * Samfile template = None,
- * referencenames = None, # <<<<<<<<<<<<<<
- * referencelengths = None,
- * text = None,
+ /* "csamtools.pyx":487
+ * else:
+ * # samtools adds a '\0' at the end
+ * seq = fai_fetch( self.fastafile, region, &length ) # <<<<<<<<<<<<<<
+ *
+ * # copy to python
*/
- __pyx_v_referencenames = ((PyObject *)Py_None);
+ __pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":477
- * Samfile template = None,
- * referencenames = None,
- * referencelengths = None, # <<<<<<<<<<<<<<
- * text = None,
- * header = None,
+ /* "csamtools.pyx":490
+ *
+ * # copy to python
+ * if seq == NULL: # <<<<<<<<<<<<<<
+ * return b""
+ * else:
*/
- __pyx_v_referencelengths = ((PyObject *)Py_None);
+ __pyx_t_3 = (__pyx_v_seq == NULL);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":478
- * referencenames = None,
- * referencelengths = None,
- * text = None, # <<<<<<<<<<<<<<
- * header = None,
- * port = None,
+ /* "csamtools.pyx":491
+ * # copy to python
+ * if seq == NULL:
+ * return b"" # <<<<<<<<<<<<<<
+ * else:
+ * try:
*/
- __pyx_v_text = ((PyObject *)Py_None);
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
+ __pyx_r = ((PyObject *)__pyx_kp_b_16);
+ goto __pyx_L0;
+ goto __pyx_L13;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":479
- * referencelengths = None,
- * text = None,
- * header = None, # <<<<<<<<<<<<<<
- * port = None,
- * ):
+ /* "csamtools.pyx":493
+ * return b""
+ * else:
+ * try: # <<<<<<<<<<<<<<
+ * py_seq = seq[:length]
+ * finally:
*/
- __pyx_v_header = ((PyObject *)Py_None);
+ /*try:*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":480
- * text = None,
- * header = None,
- * port = None, # <<<<<<<<<<<<<<
- * ):
- * '''open a sam/bam file.
+ /* "csamtools.pyx":494
+ * else:
+ * try:
+ * py_seq = seq[:length] # <<<<<<<<<<<<<<
+ * finally:
+ * free(seq)
*/
- __pyx_v_port = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 8: __pyx_v_port = PyTuple_GET_ITEM(__pyx_args, 7);
- case 7: __pyx_v_header = PyTuple_GET_ITEM(__pyx_args, 6);
- case 6: __pyx_v_text = PyTuple_GET_ITEM(__pyx_args, 5);
- case 5: __pyx_v_referencelengths = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: __pyx_v_referencenames = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 2));
- case 2: __pyx_v_mode = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_filename = PyBytes_AsString(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- break;
- default: goto __pyx_L5_argtuple_error;
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L15;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_py_seq = __pyx_t_2;
+ __pyx_t_2 = 0;
}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile._open");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_msg = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_n = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_x = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_name = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_store = Py_None; __Pyx_INCREF(Py_None);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":489
+ /* "csamtools.pyx":496
+ * py_seq = seq[:length]
+ * finally:
+ * free(seq) # <<<<<<<<<<<<<<
*
- * # read mode autodetection
- * if mode is None: # <<<<<<<<<<<<<<
- * try:
- * self._open(filename, 'r', template=template,
+ * return py_seq
*/
- __pyx_t_1 = (__pyx_v_mode == Py_None);
- if (__pyx_t_1) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":490
- * # read mode autodetection
- * if mode is None:
- * try: # <<<<<<<<<<<<<<
- * self._open(filename, 'r', template=template,
- * referencenames=referencenames,
+ /*finally:*/ {
+ int __pyx_why;
+ PyObject *__pyx_exc_type, *__pyx_exc_value, *__pyx_exc_tb;
+ int __pyx_exc_lineno;
+ __pyx_exc_type = 0; __pyx_exc_value = 0; __pyx_exc_tb = 0; __pyx_exc_lineno = 0;
+ __pyx_why = 0; goto __pyx_L16;
+ __pyx_L15: {
+ __pyx_why = 4;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_ErrFetch(&__pyx_exc_type, &__pyx_exc_value, &__pyx_exc_tb);
+ __pyx_exc_lineno = __pyx_lineno;
+ goto __pyx_L16;
+ }
+ __pyx_L16:;
+ free(__pyx_v_seq);
+ switch (__pyx_why) {
+ case 4: {
+ __Pyx_ErrRestore(__pyx_exc_type, __pyx_exc_value, __pyx_exc_tb);
+ __pyx_lineno = __pyx_exc_lineno;
+ __pyx_exc_type = 0;
+ __pyx_exc_value = 0;
+ __pyx_exc_tb = 0;
+ goto __pyx_L1_error;
+ }
+ }
+ }
+ }
+ __pyx_L13:;
+
+ /* "csamtools.pyx":498
+ * free(seq)
+ *
+ * return py_seq # <<<<<<<<<<<<<<
+ *
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length ):
*/
- {
- PyObject *__pyx_save_exc_type, *__pyx_save_exc_value, *__pyx_save_exc_tb;
- __Pyx_ExceptionSave(&__pyx_save_exc_type, &__pyx_save_exc_value, &__pyx_save_exc_tb);
- __Pyx_XGOTREF(__pyx_save_exc_type);
- __Pyx_XGOTREF(__pyx_save_exc_value);
- __Pyx_XGOTREF(__pyx_save_exc_tb);
- /*try:*/ {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_py_seq));
+ __pyx_r = ((PyObject *)__pyx_v_py_seq);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":491
- * if mode is None:
- * try:
- * self._open(filename, 'r', template=template, # <<<<<<<<<<<<<<
- * referencenames=referencenames,
- * referencelengths=referencelengths,
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_py_seq);
+ __Pyx_XDECREF(__pyx_v_start);
+ __Pyx_XDECREF(__pyx_v_end);
+ __Pyx_XDECREF(__pyx_v_region);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":500
+ * return py_seq
+ *
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length ): # <<<<<<<<<<<<<<
+ * '''fetch sequence for reference, start and end'''
+ *
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":492
- * try:
- * self._open(filename, 'r', template=template,
- * referencenames=referencenames, # <<<<<<<<<<<<<<
- * referencelengths=referencelengths,
- * text=text, header=header, port=port)
+static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, char *__pyx_v_reference, int __pyx_v_start, int __pyx_v_end, int *__pyx_v_length) {
+ char *__pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_fetch", 0);
+ __Pyx_TraceCall("_fetch", __pyx_f[0], 500);
+
+ /* "csamtools.pyx":507
+ * start,
+ * end-1,
+ * length ) # <<<<<<<<<<<<<<
+ *
+ * #------------------------------------------------------------------------
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __pyx_r = faidx_fetch_seq(__pyx_v_self->fastafile, __pyx_v_reference, __pyx_v_start, (__pyx_v_end - 1), __pyx_v_length);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":493
- * self._open(filename, 'r', template=template,
- * referencenames=referencenames,
- * referencelengths=referencelengths, # <<<<<<<<<<<<<<
- * text=text, header=header, port=port)
- * return
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":512
+ * #------------------------------------------------------------------------
+ * #------------------------------------------------------------------------
+ * cdef int count_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
+ * '''callback for bam_fetch - count number of reads.
+ * '''
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":494
- * referencenames=referencenames,
- * referencelengths=referencelengths,
- * text=text, header=header, port=port) # <<<<<<<<<<<<<<
- * return
- * except ValueError, msg:
+static int __pyx_f_9csamtools_count_callback(CYTHON_UNUSED bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+ int *__pyx_v_counter;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ long __pyx_t_1;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("count_callback", 0);
+ __Pyx_TraceCall("count_callback", __pyx_f[0], 512);
+
+ /* "csamtools.pyx":515
+ * '''callback for bam_fetch - count number of reads.
+ * '''
+ * cdef int* counter = (<int*>f) # <<<<<<<<<<<<<<
+ * counter[0] += 1;
+ *
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, __pyx_t_4, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_v_counter = ((int *)__pyx_v_f);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":495
- * referencelengths=referencelengths,
- * text=text, header=header, port=port)
- * return # <<<<<<<<<<<<<<
- * except ValueError, msg:
- * pass
+ /* "csamtools.pyx":516
+ * '''
+ * cdef int* counter = (<int*>f)
+ * counter[0] += 1; # <<<<<<<<<<<<<<
+ *
+ * ctypedef struct MateData:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L11_try_return;
- }
- __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0;
- __Pyx_XDECREF(__pyx_save_exc_value); __pyx_save_exc_value = 0;
- __Pyx_XDECREF(__pyx_save_exc_tb); __pyx_save_exc_tb = 0;
- goto __pyx_L14_try_end;
- __pyx_L11_try_return:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- goto __pyx_L0;
- __pyx_L7_error:;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = 0;
+ (__pyx_v_counter[__pyx_t_1]) = ((__pyx_v_counter[__pyx_t_1]) + 1);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":496
- * text=text, header=header, port=port)
- * return
- * except ValueError, msg: # <<<<<<<<<<<<<<
- * pass
- * self._open(filename, 'rb', template=template,
+ __pyx_r = 0;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":526
+ * #------------------------------------------------------------------------
+ * #------------------------------------------------------------------------
+ * cdef int mate_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
+ * '''callback for bam_fetch = filter mate
+ * '''
*/
- __pyx_t_6 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
- if (__pyx_t_6) {
- __Pyx_AddTraceback("csamtools.Samfile._open");
- if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_3, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_v_msg);
- __pyx_v_msg = __pyx_t_3;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L8_exception_handled;
- }
- __pyx_L9_except_error:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- goto __pyx_L1_error;
- __pyx_L8_exception_handled:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- __pyx_L14_try_end:;
- }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":498
- * except ValueError, msg:
- * pass
- * self._open(filename, 'rb', template=template, # <<<<<<<<<<<<<<
- * referencenames=referencenames,
- * referencelengths=referencelengths,
+static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+ __pyx_t_9csamtools_MateData *__pyx_v_d;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("mate_callback", 0);
+ __Pyx_TraceCall("mate_callback", __pyx_f[0], 526);
+
+ /* "csamtools.pyx":529
+ * '''callback for bam_fetch = filter mate
+ * '''
+ * cdef MateData * d = (<MateData*>f) # <<<<<<<<<<<<<<
+ * # printf("mate = %p, name1 = %s, name2=%s\t%i\t%i\t%i\n",
+ * # d.mate, d.name, bam1_qname(alignment),
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- PyTuple_SET_ITEM(__pyx_t_5, 1, ((PyObject *)__pyx_n_s__rb));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_d = ((__pyx_t_9csamtools_MateData *)__pyx_v_f);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":499
- * pass
- * self._open(filename, 'rb', template=template,
- * referencenames=referencenames, # <<<<<<<<<<<<<<
- * referencelengths=referencelengths,
- * text=text, header=header, port=port)
+ /* "csamtools.pyx":534
+ * # d.flag, alignment.core.flag, alignment.core.flag & d.flag)
+ *
+ * if d.mate == NULL: # <<<<<<<<<<<<<<
+ * # could be sped up by comparing the lengths of query strings first
+ * # using l_qname
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_v_d->mate == NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":500
- * self._open(filename, 'rb', template=template,
- * referencenames=referencenames,
- * referencelengths=referencelengths, # <<<<<<<<<<<<<<
- * text=text, header=header, port=port)
- * return
+ /* "csamtools.pyx":540
+ * # also, make sure that we get the other read by comparing
+ * # the flags
+ * if alignment.core.flag & d.flag != 0 and \ # <<<<<<<<<<<<<<
+ * strcmp( bam1_qname( alignment ), d.name ) == 0:
+ * d.mate = bam_dup1( alignment )
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((__pyx_v_alignment->core.flag & __pyx_v_d->flag) != 0);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":501
- * referencenames=referencenames,
- * referencelengths=referencelengths,
- * text=text, header=header, port=port) # <<<<<<<<<<<<<<
- * return
+ /* "csamtools.pyx":541
+ * # the flags
+ * if alignment.core.flag & d.flag != 0 and \
+ * strcmp( bam1_qname( alignment ), d.name ) == 0: # <<<<<<<<<<<<<<
+ * d.mate = bam_dup1( alignment )
*
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_4, __pyx_t_5, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = (strcmp(bam1_qname(__pyx_v_alignment), __pyx_v_d->name) == 0);
+ __pyx_t_3 = __pyx_t_2;
+ } else {
+ __pyx_t_3 = __pyx_t_1;
+ }
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":502
- * referencelengths=referencelengths,
- * text=text, header=header, port=port)
- * return # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":542
+ * if alignment.core.flag & d.flag != 0 and \
+ * strcmp( bam1_qname( alignment ), d.name ) == 0:
+ * d.mate = bam_dup1( alignment ) # <<<<<<<<<<<<<<
+ *
*
- * assert mode in ( "r","w","rb","wb", "wh", "wbu" ), "invalid file opening mode `%s`" % mode
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- goto __pyx_L6;
+ __pyx_v_d->mate = bam_dup1(__pyx_v_alignment);
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":504
- * return
- *
- * assert mode in ( "r","w","rb","wb", "wh", "wbu" ), "invalid file opening mode `%s`" % mode # <<<<<<<<<<<<<<
- * assert filename != NULL
+ __pyx_r = 0;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
+ __pyx_r = __pyx_pf_9csamtools_7Samfile___cinit__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":592
+ * '''
*
+ * def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
+ * self.samfile = NULL
+ * self._filename = NULL
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __Pyx_INCREF(__pyx_v_mode);
- __pyx_t_2 = __pyx_v_mode;
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __pyx_t_1;
- if (!__pyx_t_7) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __pyx_t_1;
- __pyx_t_1 = __pyx_t_8;
- } else {
- __pyx_t_1 = __pyx_t_7;
- }
- if (!__pyx_t_1) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__rb), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __pyx_t_7;
- __pyx_t_7 = __pyx_t_8;
- } else {
- __pyx_t_7 = __pyx_t_1;
- }
- if (!__pyx_t_7) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__wb), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __pyx_t_1;
- __pyx_t_1 = __pyx_t_8;
- } else {
- __pyx_t_1 = __pyx_t_7;
- }
- if (!__pyx_t_1) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__wh), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __pyx_t_7;
- __pyx_t_7 = __pyx_t_8;
- } else {
- __pyx_t_7 = __pyx_t_1;
- }
- if (!__pyx_t_7) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__wbu), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __pyx_t_1;
- __pyx_t_1 = __pyx_t_8;
- } else {
- __pyx_t_1 = __pyx_t_7;
- }
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(!__pyx_t_1)) {
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_12), __pyx_v_mode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_2));
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":505
- *
- * assert mode in ( "r","w","rb","wb", "wh", "wbu" ), "invalid file opening mode `%s`" % mode
- * assert filename != NULL # <<<<<<<<<<<<<<
- *
- * # close a previously opened file
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_filename != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 592);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":508
- *
- * # close a previously opened file
- * if self.samfile != NULL: self.close() # <<<<<<<<<<<<<<
- * self.samfile = NULL
+ /* "csamtools.pyx":593
*
- */
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
- if (__pyx_t_1) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L17;
- }
- __pyx_L17:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":509
- * # close a previously opened file
- * if self.samfile != NULL: self.close()
+ * def __cinit__(self, *args, **kwargs ):
* self.samfile = NULL # <<<<<<<<<<<<<<
- *
- * cdef bam_header_t * header_to_write
+ * self._filename = NULL
+ * self.isbam = False
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
+ __pyx_v_self->samfile = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":512
- *
- * cdef bam_header_t * header_to_write
- * header_to_write = NULL # <<<<<<<<<<<<<<
- *
- * if self._filename != NULL: free(self._filename )
+ /* "csamtools.pyx":594
+ * def __cinit__(self, *args, **kwargs ):
+ * self.samfile = NULL
+ * self._filename = NULL # <<<<<<<<<<<<<<
+ * self.isbam = False
+ * self.isstream = False
*/
- __pyx_v_header_to_write = NULL;
+ __pyx_v_self->_filename = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":514
- * header_to_write = NULL
- *
- * if self._filename != NULL: free(self._filename ) # <<<<<<<<<<<<<<
- * self._filename = strdup( filename )
- *
+ /* "csamtools.pyx":595
+ * self.samfile = NULL
+ * self._filename = NULL
+ * self.isbam = False # <<<<<<<<<<<<<<
+ * self.isstream = False
+ * self._open( *args, **kwargs )
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
- if (__pyx_t_1) {
- free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
- goto __pyx_L18;
- }
- __pyx_L18:;
+ __pyx_v_self->isbam = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":515
- *
- * if self._filename != NULL: free(self._filename )
- * self._filename = strdup( filename ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":596
+ * self._filename = NULL
+ * self.isbam = False
+ * self.isstream = False # <<<<<<<<<<<<<<
+ * self._open( *args, **kwargs )
*
- * self.isbam = len(mode) > 1 and mode[1] == 'b'
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = strdup(__pyx_v_filename);
+ __pyx_v_self->isstream = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":517
- * self._filename = strdup( filename )
- *
- * self.isbam = len(mode) > 1 and mode[1] == 'b' # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":597
+ * self.isbam = False
+ * self.isstream = False
+ * self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
*
- * self.isremote = strncmp(filename,"http:",5) == 0 or \
+ * # allocate memory for iterator
*/
- __pyx_t_9 = PyObject_Length(__pyx_v_mode); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyBool_FromLong((__pyx_t_9 > 1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_mode, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__b), Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __pyx_t_5;
- __pyx_t_5 = 0;
- } else {
- __pyx_t_2 = __pyx_t_3;
- __pyx_t_3 = 0;
- }
- __pyx_t_6 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = __pyx_t_6;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":519
- * self.isbam = len(mode) > 1 and mode[1] == 'b'
+ /* "csamtools.pyx":600
*
- * self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
- * strncmp(filename,"ftp:",4) == 0
+ * # allocate memory for iterator
+ * self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
+ * def _isOpen( self ):
*/
- __pyx_t_1 = (strncmp(__pyx_v_filename, __pyx_k_13, 5) == 0);
- if (!__pyx_t_1) {
+ __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":520
- *
- * self.isremote = strncmp(filename,"http:",5) == 0 or \
- * strncmp(filename,"ftp:",4) == 0 # <<<<<<<<<<<<<<
- *
- * cdef char * ctext
- */
- __pyx_t_7 = (strncmp(__pyx_v_filename, __pyx_k_14, 4) == 0);
- __pyx_t_8 = __pyx_t_7;
- } else {
- __pyx_t_8 = __pyx_t_1;
- }
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":519
- * self.isbam = len(mode) > 1 and mode[1] == 'b'
- *
- * self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
- * strncmp(filename,"ftp:",4) == 0
- *
- */
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote = __pyx_t_8;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_2_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pw_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_2_isOpen(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":523
- *
- * cdef char * ctext
- * ctext = NULL # <<<<<<<<<<<<<<
+/* "csamtools.pyx":602
+ * self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
- * if mode[0] == 'w':
+ * def _isOpen( self ): # <<<<<<<<<<<<<<
+ * '''return true if samfile has been opened.'''
+ * return self.samfile != NULL
*/
- __pyx_v_ctext = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":525
- * ctext = NULL
- *
- * if mode[0] == 'w': # <<<<<<<<<<<<<<
- * # open file for writing
- *
- */
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_8) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_isOpen", 0);
+ __Pyx_TraceCall("_isOpen", __pyx_f[0], 602);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":529
+ /* "csamtools.pyx":604
+ * def _isOpen( self ):
+ * '''return true if samfile has been opened.'''
+ * return self.samfile != NULL # <<<<<<<<<<<<<<
*
- * # header structure (used for writing)
- * if template: # <<<<<<<<<<<<<<
- * # copy header from another file
- * header_to_write = template.samfile.header
+ * def _hasIndex( self ):
*/
- __pyx_t_8 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_8) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":531
- * if template:
- * # copy header from another file
- * header_to_write = template.samfile.header # <<<<<<<<<<<<<<
- *
- * elif header:
- */
- __pyx_v_header_to_write = __pyx_v_template->samfile->header;
- goto __pyx_L20;
- }
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.Samfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":533
- * header_to_write = template.samfile.header
- *
- * elif header: # <<<<<<<<<<<<<<
- * header_to_write = self._buildHeader( header )
- *
- */
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_8) {
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_4_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
+static PyObject *__pyx_pw_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_hasIndex (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_4_hasIndex(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":534
- *
- * elif header:
- * header_to_write = self._buildHeader( header ) # <<<<<<<<<<<<<<
+/* "csamtools.pyx":606
+ * return self.samfile != NULL
*
- * else:
+ * def _hasIndex( self ): # <<<<<<<<<<<<<<
+ * '''return true if samfile has an existing (and opened) index.'''
+ * return self.index != NULL
*/
- __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->_buildHeader(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_header);
- goto __pyx_L20;
- }
- /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":538
- * else:
- * # build header from a target names and lengths
- * assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" # <<<<<<<<<<<<<<
- * assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences"
- *
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_8) {
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = __pyx_t_1;
- } else {
- __pyx_t_7 = __pyx_t_8;
- }
- if (unlikely(!__pyx_t_7)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_15));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_hasIndex", 0);
+ __Pyx_TraceCall("_hasIndex", __pyx_f[0], 606);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":539
- * # build header from a target names and lengths
- * assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"
- * assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":608
+ * def _hasIndex( self ):
+ * '''return true if samfile has an existing (and opened) index.'''
+ * return self.index != NULL # <<<<<<<<<<<<<<
*
- * # allocate and fill header
+ * def _open( self,
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_9 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!(__pyx_t_9 == __pyx_t_10))) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_16));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":542
- *
- * # allocate and fill header
- * header_to_write = bam_header_init() # <<<<<<<<<<<<<<
- * header_to_write.n_targets = len(referencenames)
- * n = 0
- */
- __pyx_v_header_to_write = bam_header_init();
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.Samfile._hasIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":543
- * # allocate and fill header
- * header_to_write = bam_header_init()
- * header_to_write.n_targets = len(referencenames) # <<<<<<<<<<<<<<
- * n = 0
- * for x in referencenames: n += len(x) + 1
- */
- __pyx_t_10 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->n_targets = __pyx_t_10;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_6_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_filename = 0;
+ PyObject *__pyx_v_mode = 0;
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_template = 0;
+ PyObject *__pyx_v_referencenames = 0;
+ PyObject *__pyx_v_referencelengths = 0;
+ PyObject *__pyx_v_text = 0;
+ PyObject *__pyx_v_header = 0;
+ PyObject *__pyx_v_port = 0;
+ PyObject *__pyx_v_add_sq_text = 0;
+ PyObject *__pyx_v_check_header = 0;
+ PyObject *__pyx_v_check_sq = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_open (wrapper)", 0);
+ {
+ PyObject* values[11] = {0,0,0,0,0,0,0,0,0,0,0};
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":544
- * header_to_write = bam_header_init()
- * header_to_write.n_targets = len(referencenames)
- * n = 0 # <<<<<<<<<<<<<<
- * for x in referencenames: n += len(x) + 1
- * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
+ /* "csamtools.pyx":612
+ * def _open( self,
+ * filename,
+ * mode = None, # <<<<<<<<<<<<<<
+ * Samfile template = None,
+ * referencenames = None,
*/
- __Pyx_INCREF(__pyx_int_0);
- __Pyx_DECREF(__pyx_v_n);
- __pyx_v_n = __pyx_int_0;
+ values[1] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":545
- * header_to_write.n_targets = len(referencenames)
- * n = 0
- * for x in referencenames: n += len(x) + 1 # <<<<<<<<<<<<<<
- * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
- * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+ /* "csamtools.pyx":613
+ * filename,
+ * mode = None,
+ * Samfile template = None, # <<<<<<<<<<<<<<
+ * referencenames = None,
+ * referencelengths = None,
*/
- if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
- __pyx_t_10 = 0; __pyx_t_3 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_3);
- } else {
- __pyx_t_10 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- }
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_3))) {
- if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_3))) {
- if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++;
- } else {
- __pyx_t_2 = PyIter_Next(__pyx_t_3);
- if (!__pyx_t_2) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_2);
- }
- __Pyx_DECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_2;
- __pyx_t_2 = 0;
- __pyx_t_9 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_9 + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_v_n);
- __pyx_v_n = __pyx_t_5;
- __pyx_t_5 = 0;
- }
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ values[2] = (PyObject *)((struct __pyx_obj_9csamtools_Samfile *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":546
- * n = 0
- * for x in referencenames: n += len(x) + 1
- * header_to_write.target_name = <char**>calloc(n, sizeof(char*)) # <<<<<<<<<<<<<<
- * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
- * for x from 0 <= x < header_to_write.n_targets:
+ /* "csamtools.pyx":614
+ * mode = None,
+ * Samfile template = None,
+ * referencenames = None, # <<<<<<<<<<<<<<
+ * referencelengths = None,
+ * text = None,
*/
- __pyx_t_11 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_11 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_11, (sizeof(char *))));
+ values[3] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":547
- * for x in referencenames: n += len(x) + 1
- * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
- * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t)) # <<<<<<<<<<<<<<
- * for x from 0 <= x < header_to_write.n_targets:
- * header_to_write.target_len[x] = referencelengths[x]
+ /* "csamtools.pyx":615
+ * Samfile template = None,
+ * referencenames = None,
+ * referencelengths = None, # <<<<<<<<<<<<<<
+ * text = None,
+ * header = None,
*/
- __pyx_t_11 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_11 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_11, (sizeof(uint32_t))));
+ values[4] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":548
- * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
- * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
- * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
- * header_to_write.target_len[x] = referencelengths[x]
- * name = referencenames[x]
+ /* "csamtools.pyx":616
+ * referencenames = None,
+ * referencelengths = None,
+ * text = None, # <<<<<<<<<<<<<<
+ * header = None,
+ * port = None,
*/
- __pyx_t_12 = __pyx_v_header_to_write->n_targets;
- for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13++) {
- __pyx_t_3 = PyInt_FromLong(__pyx_t_13); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_3;
- __pyx_t_3 = 0;
+ values[5] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":549
- * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
- * for x from 0 <= x < header_to_write.n_targets:
- * header_to_write.target_len[x] = referencelengths[x] # <<<<<<<<<<<<<<
- * name = referencenames[x]
- * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
+ /* "csamtools.pyx":617
+ * referencelengths = None,
+ * text = None,
+ * header = None, # <<<<<<<<<<<<<<
+ * port = None,
+ * add_sq_text = True,
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_14 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_3); if (unlikely((__pyx_t_14 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_10 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_10 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_header_to_write->target_len[__pyx_t_10]) = __pyx_t_14;
+ values[6] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":550
- * for x from 0 <= x < header_to_write.n_targets:
- * header_to_write.target_len[x] = referencelengths[x]
- * name = referencenames[x] # <<<<<<<<<<<<<<
- * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
- * strncpy( header_to_write.target_name[x], name, len(name) )
+ /* "csamtools.pyx":618
+ * text = None,
+ * header = None,
+ * port = None, # <<<<<<<<<<<<<<
+ * add_sq_text = True,
+ * check_header = True,
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_v_name);
- __pyx_v_name = __pyx_t_3;
- __pyx_t_3 = 0;
+ values[7] = ((PyObject *)Py_None);
+ values[8] = __pyx_k_21;
+ values[9] = __pyx_k_22;
+ values[10] = __pyx_k_23;
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 11: values[10] = PyTuple_GET_ITEM(__pyx_args, 10);
+ case 10: values[9] = PyTuple_GET_ITEM(__pyx_args, 9);
+ case 9: values[8] = PyTuple_GET_ITEM(__pyx_args, 8);
+ case 8: values[7] = PyTuple_GET_ITEM(__pyx_args, 7);
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__mode);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__template);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__referencenames);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__referencelengths);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ case 5:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__text);
+ if (value) { values[5] = value; kw_args--; }
+ }
+ case 6:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header);
+ if (value) { values[6] = value; kw_args--; }
+ }
+ case 7:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__port);
+ if (value) { values[7] = value; kw_args--; }
+ }
+ case 8:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__add_sq_text);
+ if (value) { values[8] = value; kw_args--; }
+ }
+ case 9:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__check_header);
+ if (value) { values[9] = value; kw_args--; }
+ }
+ case 10:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__check_sq);
+ if (value) { values[10] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 11: values[10] = PyTuple_GET_ITEM(__pyx_args, 10);
+ case 10: values[9] = PyTuple_GET_ITEM(__pyx_args, 9);
+ case 9: values[8] = PyTuple_GET_ITEM(__pyx_args, 8);
+ case 8: values[7] = PyTuple_GET_ITEM(__pyx_args, 7);
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_filename = values[0];
+ __pyx_v_mode = values[1];
+ __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)values[2]);
+ __pyx_v_referencenames = values[3];
+ __pyx_v_referencelengths = values[4];
+ __pyx_v_text = values[5];
+ __pyx_v_header = values[6];
+ __pyx_v_port = values[7];
+ __pyx_v_add_sq_text = values[8];
+ __pyx_v_check_header = values[9];
+ __pyx_v_check_sq = values[10];
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 11, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_6_open(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_template, __pyx_v_referencenames, __pyx_v_referencelengths, __pyx_v_text, __pyx_v_header, __pyx_v_port, __pyx_v_add_sq_text, __pyx_v_check_header, __pyx_v_check_sq);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":551
- * header_to_write.target_len[x] = referencelengths[x]
- * name = referencenames[x]
- * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char)) # <<<<<<<<<<<<<<
- * strncpy( header_to_write.target_name[x], name, len(name) )
+/* "csamtools.pyx":610
+ * return self.index != NULL
*
+ * def _open( self, # <<<<<<<<<<<<<<
+ * filename,
+ * mode = None,
*/
- __pyx_t_10 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_9 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_header_to_write->target_name[__pyx_t_9]) = ((char *)calloc((__pyx_t_10 + 1), (sizeof(char))));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":552
- * name = referencenames[x]
- * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
- * strncpy( header_to_write.target_name[x], name, len(name) ) # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq) {
+ CYTHON_UNUSED PyObject *__pyx_v_msg = NULL;
+ bam_header_t *__pyx_v_header_to_write;
+ PyObject *__pyx_v_bmode = 0;
+ char *__pyx_v_ctext;
+ PyObject *__pyx_v_n = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_name = NULL;
+ PyObject *__pyx_v_store = NULL;
+ PyObject *__pyx_v_ref = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_t_11;
+ char *__pyx_t_12;
+ Py_ssize_t __pyx_t_13;
+ Py_ssize_t __pyx_t_14;
+ PyObject *(*__pyx_t_15)(PyObject *);
+ size_t __pyx_t_16;
+ int32_t __pyx_t_17;
+ long __pyx_t_18;
+ uint32_t __pyx_t_19;
+ const char* __pyx_t_20;
+ int __pyx_t_21;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_open", 0);
+ __Pyx_TraceCall("_open", __pyx_f[0], 610);
+ __Pyx_INCREF(__pyx_v_filename);
+ __Pyx_INCREF(__pyx_v_referencenames);
+ __Pyx_INCREF(__pyx_v_text);
+
+ /* "csamtools.pyx":630
*
- * if text != None:
+ * # read mode autodetection
+ * if mode is None: # <<<<<<<<<<<<<<
+ * try:
+ * self._open(filename, 'rb', template=template,
*/
- __pyx_t_10 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_10 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_15 = PyBytes_AsString(__pyx_v_name); if (unlikely((!__pyx_t_15) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy((__pyx_v_header_to_write->target_name[__pyx_t_10]), __pyx_t_15, __pyx_t_9);
- __pyx_t_13 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_13 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
+ __pyx_t_1 = (__pyx_v_mode == Py_None);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":548
- * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
- * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
- * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
- * header_to_write.target_len[x] = referencelengths[x]
- * name = referencenames[x]
+ /* "csamtools.pyx":631
+ * # read mode autodetection
+ * if mode is None:
+ * try: # <<<<<<<<<<<<<<
+ * self._open(filename, 'rb', template=template,
+ * referencenames=referencenames,
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_t_13); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_3;
- __pyx_t_3 = 0;
+ {
+ __Pyx_ExceptionSave(&__pyx_t_2, &__pyx_t_3, &__pyx_t_4);
+ __Pyx_XGOTREF(__pyx_t_2);
+ __Pyx_XGOTREF(__pyx_t_3);
+ __Pyx_XGOTREF(__pyx_t_4);
+ /*try:*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":554
- * strncpy( header_to_write.target_name[x], name, len(name) )
- *
- * if text != None: # <<<<<<<<<<<<<<
- * # copy without \0
- * ctext = text
+ /* "csamtools.pyx":632
+ * if mode is None:
+ * try:
+ * self._open(filename, 'rb', template=template, # <<<<<<<<<<<<<<
+ * referencenames=referencenames,
+ * referencelengths=referencelengths,
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_text, Py_None, Py_NE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_7) {
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_filename);
+ __Pyx_GIVEREF(__pyx_v_filename);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":556
- * if text != None:
- * # copy without \0
- * ctext = text # <<<<<<<<<<<<<<
- * header_to_write.l_text = strlen(ctext)
- * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
+ /* "csamtools.pyx":633
+ * try:
+ * self._open(filename, 'rb', template=template,
+ * referencenames=referencenames, # <<<<<<<<<<<<<<
+ * referencelengths=referencelengths,
+ * text=text, header=header, port=port,
*/
- __pyx_t_15 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_15) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_ctext = __pyx_t_15;
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":557
- * # copy without \0
- * ctext = text
- * header_to_write.l_text = strlen(ctext) # <<<<<<<<<<<<<<
- * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
- * memcpy( header_to_write.text, ctext, strlen(ctext) )
+ /* "csamtools.pyx":634
+ * self._open(filename, 'rb', template=template,
+ * referencenames=referencenames,
+ * referencelengths=referencelengths, # <<<<<<<<<<<<<<
+ * text=text, header=header, port=port,
+ * check_header=check_header,
*/
- __pyx_v_header_to_write->l_text = strlen(__pyx_v_ctext);
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":558
- * ctext = text
- * header_to_write.l_text = strlen(ctext)
- * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) ) # <<<<<<<<<<<<<<
- * memcpy( header_to_write.text, ctext, strlen(ctext) )
- *
+ /* "csamtools.pyx":635
+ * referencenames=referencenames,
+ * referencelengths=referencelengths,
+ * text=text, header=header, port=port, # <<<<<<<<<<<<<<
+ * check_header=check_header,
+ * check_sq=check_sq)
*/
- __pyx_v_header_to_write->text = ((char *)calloc(strlen(__pyx_v_ctext), (sizeof(char))));
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":559
- * header_to_write.l_text = strlen(ctext)
- * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
- * memcpy( header_to_write.text, ctext, strlen(ctext) ) # <<<<<<<<<<<<<<
- *
- * header_to_write.hash = NULL
+ /* "csamtools.pyx":636
+ * referencelengths=referencelengths,
+ * text=text, header=header, port=port,
+ * check_header=check_header, # <<<<<<<<<<<<<<
+ * check_sq=check_sq)
+ * return
*/
- memcpy(__pyx_v_header_to_write->text, __pyx_v_ctext, strlen(__pyx_v_ctext));
- goto __pyx_L25;
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+
+ /* "csamtools.pyx":637
+ * text=text, header=header, port=port,
+ * check_header=check_header,
+ * check_sq=check_sq) # <<<<<<<<<<<<<<
+ * return
+ * except ValueError, msg:
+ */
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+
+ /* "csamtools.pyx":638
+ * check_header=check_header,
+ * check_sq=check_sq)
+ * return # <<<<<<<<<<<<<<
+ * except ValueError, msg:
+ * pass
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L8_try_return;
}
- __pyx_L25:;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ goto __pyx_L11_try_end;
+ __pyx_L8_try_return:;
+ __Pyx_XGIVEREF(__pyx_t_2);
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
+ goto __pyx_L0;
+ __pyx_L4_error:;
+ __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":561
- * memcpy( header_to_write.text, ctext, strlen(ctext) )
- *
- * header_to_write.hash = NULL # <<<<<<<<<<<<<<
- * header_to_write.rg2lib = NULL
+ /* "csamtools.pyx":639
+ * check_sq=check_sq)
+ * return
+ * except ValueError, msg: # <<<<<<<<<<<<<<
+ * pass
*
*/
- __pyx_v_header_to_write->hash = NULL;
+ __pyx_t_9 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
+ if (__pyx_t_9) {
+ __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_v_msg = __pyx_t_7;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L5_exception_handled;
+ }
+ __pyx_L6_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_2);
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
+ goto __pyx_L1_error;
+ __pyx_L5_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_2);
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
+ __pyx_L11_try_end:;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":562
+ /* "csamtools.pyx":642
+ * pass
*
- * header_to_write.hash = NULL
- * header_to_write.rg2lib = NULL # <<<<<<<<<<<<<<
+ * self._open(filename, 'r', template=template, # <<<<<<<<<<<<<<
+ * referencenames=referencenames,
+ * referencelengths=referencelengths,
+ */
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
+ __Pyx_GIVEREF(__pyx_v_filename);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_7, 1, ((PyObject *)__pyx_n_s__r));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":643
*
- * # open file. Header gets written to file at the same time for bam files
+ * self._open(filename, 'r', template=template,
+ * referencenames=referencenames, # <<<<<<<<<<<<<<
+ * referencelengths=referencelengths,
+ * text=text, header=header, port=port,
*/
- __pyx_v_header_to_write->rg2lib = NULL;
- }
- __pyx_L20:;
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":566
- * # open file. Header gets written to file at the same time for bam files
- * # and sam files (in the latter case, the mode needs to be wh)
- * store = StderrStore() # <<<<<<<<<<<<<<
- * self.samfile = samopen( filename, mode, header_to_write )
- * store.release()
+ /* "csamtools.pyx":644
+ * self._open(filename, 'r', template=template,
+ * referencenames=referencenames,
+ * referencelengths=referencelengths, # <<<<<<<<<<<<<<
+ * text=text, header=header, port=port,
+ * check_header=check_header,
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_store);
- __pyx_v_store = __pyx_t_5;
- __pyx_t_5 = 0;
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":567
- * # and sam files (in the latter case, the mode needs to be wh)
- * store = StderrStore()
- * self.samfile = samopen( filename, mode, header_to_write ) # <<<<<<<<<<<<<<
- * store.release()
- *
+ /* "csamtools.pyx":645
+ * referencenames=referencenames,
+ * referencelengths=referencelengths,
+ * text=text, header=header, port=port, # <<<<<<<<<<<<<<
+ * check_header=check_header,
+ * check_sq=check_sq)
*/
- __pyx_t_15 = PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_15) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_v_filename, __pyx_t_15, __pyx_v_header_to_write);
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":568
- * store = StderrStore()
- * self.samfile = samopen( filename, mode, header_to_write )
- * store.release() # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":646
+ * referencelengths=referencelengths,
+ * text=text, header=header, port=port,
+ * check_header=check_header, # <<<<<<<<<<<<<<
+ * check_sq=check_sq)
+ * return
+ */
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":647
+ * text=text, header=header, port=port,
+ * check_header=check_header,
+ * check_sq=check_sq) # <<<<<<<<<<<<<<
+ * return
*
- * # bam_header_destroy takes care of cleaning up of all the members
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":571
- *
- * # bam_header_destroy takes care of cleaning up of all the members
- * if not template and header_to_write != NULL: # <<<<<<<<<<<<<<
- * bam_header_destroy( header_to_write )
+ /* "csamtools.pyx":648
+ * check_header=check_header,
+ * check_sq=check_sq)
+ * return # <<<<<<<<<<<<<<
*
+ * assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = (!__pyx_t_7);
- if (__pyx_t_8) {
- __pyx_t_7 = (__pyx_v_header_to_write != NULL);
- __pyx_t_1 = __pyx_t_7;
- } else {
- __pyx_t_1 = __pyx_t_8;
- }
- if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":572
- * # bam_header_destroy takes care of cleaning up of all the members
- * if not template and header_to_write != NULL:
- * bam_header_destroy( header_to_write ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":650
+ * return
*
- * elif mode[0] == "r":
+ * assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode # <<<<<<<<<<<<<<
+ *
+ * #assert filename != NULL
*/
- bam_header_destroy(__pyx_v_header_to_write);
- goto __pyx_L26;
- }
- __pyx_L26:;
- goto __pyx_L19;
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ __Pyx_INCREF(__pyx_v_mode);
+ __pyx_t_5 = __pyx_v_mode;
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!((int)__pyx_t_1)) {
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = ((int)__pyx_t_10);
+ } else {
+ __pyx_t_11 = ((int)__pyx_t_1);
+ }
+ if (!__pyx_t_11) {
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__rb), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = ((int)__pyx_t_1);
+ } else {
+ __pyx_t_10 = __pyx_t_11;
+ }
+ if (!__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wb), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((int)__pyx_t_11);
+ } else {
+ __pyx_t_1 = __pyx_t_10;
}
+ if (!__pyx_t_1) {
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wh), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = ((int)__pyx_t_10);
+ } else {
+ __pyx_t_11 = __pyx_t_1;
+ }
+ if (!__pyx_t_11) {
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wbu), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = ((int)__pyx_t_1);
+ } else {
+ __pyx_t_10 = __pyx_t_11;
+ }
+ if (!__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__rU), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((int)__pyx_t_11);
+ } else {
+ __pyx_t_1 = __pyx_t_10;
+ }
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (unlikely(!__pyx_t_1)) {
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_24), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_5));
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":574
- * bam_header_destroy( header_to_write )
+ /* "csamtools.pyx":655
+ *
+ * # close a previously opened file
+ * if self.samfile != NULL: self.close() # <<<<<<<<<<<<<<
+ * self.samfile = NULL
*
- * elif mode[0] == "r": # <<<<<<<<<<<<<<
- * # open file for reading
- * if strncmp( filename, "-", 1) != 0 and \
*/
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = (__pyx_v_self->samfile != NULL);
if (__pyx_t_1) {
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ goto __pyx_L14;
+ }
+ __pyx_L14:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":576
- * elif mode[0] == "r":
- * # open file for reading
- * if strncmp( filename, "-", 1) != 0 and \ # <<<<<<<<<<<<<<
- * not self.isremote and \
- * not os.path.exists( filename ):
+ /* "csamtools.pyx":656
+ * # close a previously opened file
+ * if self.samfile != NULL: self.close()
+ * self.samfile = NULL # <<<<<<<<<<<<<<
+ *
+ * cdef bam_header_t * header_to_write
*/
- __pyx_t_1 = (strncmp(__pyx_v_filename, __pyx_k_17, 1) != 0);
- if (__pyx_t_1) {
+ __pyx_v_self->samfile = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":577
- * # open file for reading
- * if strncmp( filename, "-", 1) != 0 and \
- * not self.isremote and \ # <<<<<<<<<<<<<<
- * not os.path.exists( filename ):
- * raise IOError( "file `%s` not found" % filename)
+ /* "csamtools.pyx":659
+ *
+ * cdef bam_header_t * header_to_write
+ * header_to_write = NULL # <<<<<<<<<<<<<<
+ *
+ * if self._filename != NULL: free(self._filename )
*/
- __pyx_t_8 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
- if (__pyx_t_8) {
+ __pyx_v_header_to_write = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":578
- * if strncmp( filename, "-", 1) != 0 and \
- * not self.isremote and \
- * not os.path.exists( filename ): # <<<<<<<<<<<<<<
- * raise IOError( "file `%s` not found" % filename)
+ /* "csamtools.pyx":661
+ * header_to_write = NULL
*
+ * if self._filename != NULL: free(self._filename ) # <<<<<<<<<<<<<<
+ * filename = _my_encodeFilename(filename)
+ * cdef bytes bmode = mode.encode('ascii')
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_5, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_16 = (!__pyx_t_7);
- __pyx_t_7 = __pyx_t_16;
- } else {
- __pyx_t_7 = __pyx_t_8;
- }
- __pyx_t_8 = __pyx_t_7;
- } else {
- __pyx_t_8 = __pyx_t_1;
- }
- if (__pyx_t_8) {
+ __pyx_t_1 = (__pyx_v_self->_filename != NULL);
+ if (__pyx_t_1) {
+ free(__pyx_v_self->_filename);
+ goto __pyx_L15;
+ }
+ __pyx_L15:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":579
- * not self.isremote and \
- * not os.path.exists( filename ):
- * raise IOError( "file `%s` not found" % filename) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":662
*
- * # try to detect errors
+ * if self._filename != NULL: free(self._filename )
+ * filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<<
+ * cdef bytes bmode = mode.encode('ascii')
+ * #cdef char* cfilename
*/
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L27;
- }
- __pyx_L27:;
+ __pyx_t_8 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_v_filename);
+ __pyx_v_filename = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":582
- *
- * # try to detect errors
- * self.samfile = samopen( filename, mode, NULL ) # <<<<<<<<<<<<<<
- * if self.samfile == NULL:
- * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
+ /* "csamtools.pyx":663
+ * if self._filename != NULL: free(self._filename )
+ * filename = _my_encodeFilename(filename)
+ * cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<<
+ * #cdef char* cfilename
+ * #cfilename = filename.encode(_FILENAME_ENCODING)
*/
- __pyx_t_15 = PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_15) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_v_filename, __pyx_t_15, NULL);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_mode, __pyx_n_s__encode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_25), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (!(likely(PyBytes_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_bmode = ((PyObject*)__pyx_t_5);
+ __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":583
- * # try to detect errors
- * self.samfile = samopen( filename, mode, NULL )
- * if self.samfile == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
+ /* "csamtools.pyx":666
+ * #cdef char* cfilename
+ * #cfilename = filename.encode(_FILENAME_ENCODING)
+ * self._filename = strdup(filename) # <<<<<<<<<<<<<<
+ * self.isstream = strcmp( filename, "-" ) == 0
*
*/
- __pyx_t_8 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
- if (__pyx_t_8) {
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_filename = strdup(__pyx_t_12);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":584
- * self.samfile = samopen( filename, mode, NULL )
- * if self.samfile == NULL:
- * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":667
+ * #cfilename = filename.encode(_FILENAME_ENCODING)
+ * self._filename = strdup(filename)
+ * self.isstream = strcmp( filename, "-" ) == 0 # <<<<<<<<<<<<<<
*
- * if self.samfile.header == NULL:
+ * self.isbam = len(mode) > 1 and mode[1] == 'b'
*/
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), __pyx_v_mode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L28;
- }
- __pyx_L28:;
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":586
- * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
+ /* "csamtools.pyx":669
+ * self.isstream = strcmp( filename, "-" ) == 0
*
- * if self.samfile.header == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "file does not have valid header (mode='%s') - is it SAM/BAM format?" % mode )
+ * self.isbam = len(mode) > 1 and mode[1] == 'b' # <<<<<<<<<<<<<<
*
+ * self.isremote = strncmp(filename,"http:",5) == 0 or \
*/
- __pyx_t_8 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
- if (__pyx_t_8) {
+ __pyx_t_13 = PyObject_Length(__pyx_v_mode); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_t_13 > 1);
+ if (__pyx_t_1) {
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__b), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_11 = __pyx_t_10;
+ } else {
+ __pyx_t_11 = __pyx_t_1;
+ }
+ __pyx_v_self->isbam = __pyx_t_11;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":587
+ /* "csamtools.pyx":671
+ * self.isbam = len(mode) > 1 and mode[1] == 'b'
*
- * if self.samfile.header == NULL:
- * raise ValueError( "file does not have valid header (mode='%s') - is it SAM/BAM format?" % mode ) # <<<<<<<<<<<<<<
+ * self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
+ * strncmp(filename,"ftp:",4) == 0
*
- * #disabled for autodetection to work
*/
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_20), __pyx_v_mode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L29;
- }
- __pyx_L29:;
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = (strncmp(__pyx_t_12, __pyx_k_27, 5) == 0);
+ if (!__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":590
+ /* "csamtools.pyx":672
*
- * #disabled for autodetection to work
- * if self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
- * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
- *
- */
- __pyx_t_8 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
- if (__pyx_t_8) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":591
- * #disabled for autodetection to work
- * if self.samfile.header.n_targets == 0:
- * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
+ * self.isremote = strncmp(filename,"http:",5) == 0 or \
+ * strncmp(filename,"ftp:",4) == 0 # <<<<<<<<<<<<<<
*
- * if self.samfile == NULL:
+ * cdef char * ctext
*/
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), __pyx_v_mode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L30;
- }
- __pyx_L30:;
- goto __pyx_L19;
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (strncmp(__pyx_t_12, __pyx_k_28, 4) == 0);
+ __pyx_t_10 = __pyx_t_1;
+ } else {
+ __pyx_t_10 = __pyx_t_11;
}
- __pyx_L19:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":593
- * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
+ /* "csamtools.pyx":671
+ * self.isbam = len(mode) > 1 and mode[1] == 'b'
*
- * if self.samfile == NULL: # <<<<<<<<<<<<<<
- * raise IOError("could not open file `%s`" % filename )
+ * self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
+ * strncmp(filename,"ftp:",4) == 0
*
*/
- __pyx_t_8 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
- if (__pyx_t_8) {
+ __pyx_v_self->isremote = __pyx_t_10;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":594
+ /* "csamtools.pyx":675
*
- * if self.samfile == NULL:
- * raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
+ * cdef char * ctext
+ * ctext = NULL # <<<<<<<<<<<<<<
*
- * # check for index and open if present
+ * if mode[0] == 'w':
*/
- __pyx_t_2 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_4), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L31;
- }
- __pyx_L31:;
+ __pyx_v_ctext = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":597
+ /* "csamtools.pyx":677
+ * ctext = NULL
*
- * # check for index and open if present
- * if mode[0] == "r" and self.isbam: # <<<<<<<<<<<<<<
+ * if mode[0] == 'w': # <<<<<<<<<<<<<<
+ * # open file for writing
*
- * if not self.isremote:
*/
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_8) {
- __pyx_t_1 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam;
- } else {
- __pyx_t_1 = __pyx_t_8;
- }
- if (__pyx_t_1) {
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":599
- * if mode[0] == "r" and self.isbam:
+ /* "csamtools.pyx":681
*
- * if not self.isremote: # <<<<<<<<<<<<<<
- * if not os.path.exists(filename +".bai"):
- * self.index = NULL
+ * # header structure (used for writing)
+ * if template: # <<<<<<<<<<<<<<
+ * # copy header from another file
+ * header_to_write = template.samfile.header
*/
- __pyx_t_1 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
- if (__pyx_t_1) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":600
+ /* "csamtools.pyx":683
+ * if template:
+ * # copy header from another file
+ * header_to_write = template.samfile.header # <<<<<<<<<<<<<<
*
- * if not self.isremote:
- * if not os.path.exists(filename +".bai"): # <<<<<<<<<<<<<<
- * self.index = NULL
- * else:
- */
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_5 = PyNumber_Add(((PyObject *)__pyx_t_3), ((PyObject *)__pyx_kp_s_22)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_8 = (!__pyx_t_1);
- if (__pyx_t_8) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":601
- * if not self.isremote:
- * if not os.path.exists(filename +".bai"):
- * self.index = NULL # <<<<<<<<<<<<<<
- * else:
- * # returns NULL if there is no index or index could not be opened
- */
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = NULL;
- goto __pyx_L34;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":604
- * else:
- * # returns NULL if there is no index or index could not be opened
- * self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
- * if self.index == NULL:
- * raise IOError("error while opening index `%s` " % filename )
+ * elif header:
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_v_filename);
+ __pyx_v_header_to_write = __pyx_v_template->samfile->header;
+ goto __pyx_L17;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":605
- * # returns NULL if there is no index or index could not be opened
- * self.index = bam_index_load(filename)
- * if self.index == NULL: # <<<<<<<<<<<<<<
- * raise IOError("error while opening index `%s` " % filename )
- * else:
+ /* "csamtools.pyx":685
+ * header_to_write = template.samfile.header
+ *
+ * elif header: # <<<<<<<<<<<<<<
+ * header_to_write = self._buildHeader( header )
+ *
*/
- __pyx_t_8 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
- if (__pyx_t_8) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":606
- * self.index = bam_index_load(filename)
- * if self.index == NULL:
- * raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":686
+ *
+ * elif header:
+ * header_to_write = self._buildHeader( header ) # <<<<<<<<<<<<<<
+ *
* else:
- * self.index = bam_index_load(filename)
*/
- __pyx_t_5 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_23), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L35;
- }
- __pyx_L35:;
- }
- __pyx_L34:;
- goto __pyx_L33;
+ __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->_buildHeader(__pyx_v_self, __pyx_v_header);
+ goto __pyx_L17;
}
/*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":608
- * raise IOError("error while opening index `%s` " % filename )
+ /* "csamtools.pyx":690
* else:
- * self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
- * if self.index == NULL:
- * raise IOError("error while opening index `%s` " % filename )
+ * # build header from a target names and lengths
+ * assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" # <<<<<<<<<<<<<<
+ * assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences"
+ *
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_v_filename);
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_t_11;
+ } else {
+ __pyx_t_1 = __pyx_t_10;
+ }
+ if (unlikely(!__pyx_t_1)) {
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_29));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":609
- * else:
- * self.index = bam_index_load(filename)
- * if self.index == NULL: # <<<<<<<<<<<<<<
- * raise IOError("error while opening index `%s` " % filename )
+ /* "csamtools.pyx":691
+ * # build header from a target names and lengths
+ * assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"
+ * assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" # <<<<<<<<<<<<<<
*
+ * # allocate and fill header
*/
- __pyx_t_8 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
- if (__pyx_t_8) {
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ __pyx_t_13 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!(__pyx_t_13 == __pyx_t_14))) {
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_30));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":610
- * self.index = bam_index_load(filename)
- * if self.index == NULL:
- * raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":694
*
- * def gettid( self, reference ):
+ * # allocate and fill header
+ * referencenames = [ _force_bytes(ref) for ref in referencenames ] # <<<<<<<<<<<<<<
+ * header_to_write = bam_header_init()
+ * header_to_write.n_targets = len(referencenames)
*/
- __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_23), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L36;
+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
+ __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0;
+ __pyx_t_15 = NULL;
+ } else {
+ __pyx_t_14 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
- __pyx_L36:;
- }
- __pyx_L33:;
- goto __pyx_L32;
- }
- __pyx_L32:;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.Samfile._open");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_msg);
- __Pyx_DECREF(__pyx_v_n);
- __Pyx_DECREF(__pyx_v_x);
- __Pyx_DECREF(__pyx_v_name);
- __Pyx_DECREF(__pyx_v_store);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ for (;;) {
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
+ } else {
+ __pyx_t_7 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_7)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_7);
+ }
+ __Pyx_XDECREF(__pyx_v_ref);
+ __pyx_v_ref = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_5));
+ __Pyx_DECREF(__pyx_v_referencenames);
+ __pyx_v_referencenames = ((PyObject *)__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":612
- * raise IOError("error while opening index `%s` " % filename )
- *
- * def gettid( self, reference ): # <<<<<<<<<<<<<<
- * '''
- * convert :term:`reference` name into numerical :term:`tid`
+ /* "csamtools.pyx":695
+ * # allocate and fill header
+ * referencenames = [ _force_bytes(ref) for ref in referencenames ]
+ * header_to_write = bam_header_init() # <<<<<<<<<<<<<<
+ * header_to_write.n_targets = len(referencenames)
+ * n = 0
*/
+ __pyx_v_header_to_write = bam_header_init();
-static PyObject *__pyx_pf_9csamtools_7Samfile_gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("gettid");
- __Pyx_TraceCall("gettid", __pyx_f[0], 612);
+ /* "csamtools.pyx":696
+ * referencenames = [ _force_bytes(ref) for ref in referencenames ]
+ * header_to_write = bam_header_init()
+ * header_to_write.n_targets = len(referencenames) # <<<<<<<<<<<<<<
+ * n = 0
+ * for x in referencenames: n += len(x) + 1
+ */
+ __pyx_t_14 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->n_targets = __pyx_t_14;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":618
- * returns -1 if reference is not known.
- * '''
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * return pysam_reference2tid( self.samfile.header, reference )
- *
+ /* "csamtools.pyx":697
+ * header_to_write = bam_header_init()
+ * header_to_write.n_targets = len(referencenames)
+ * n = 0 # <<<<<<<<<<<<<<
+ * for x in referencenames: n += len(x) + 1
+ * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __Pyx_INCREF(__pyx_int_0);
+ __pyx_v_n = __pyx_int_0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":619
- * '''
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return pysam_reference2tid( self.samfile.header, reference ) # <<<<<<<<<<<<<<
- *
- * def getrname( self, tid ):
+ /* "csamtools.pyx":698
+ * header_to_write.n_targets = len(referencenames)
+ * n = 0
+ * for x in referencenames: n += len(x) + 1 # <<<<<<<<<<<<<<
+ * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
+ * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PyInt_FromLong(pysam_reference2tid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
+ __pyx_t_5 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0;
+ __pyx_t_15 = NULL;
+ } else {
+ __pyx_t_14 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_15 = Py_TYPE(__pyx_t_5)->tp_iternext;
+ }
+ for (;;) {
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_5)) {
+ if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_5)) {
+ if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
+ } else {
+ __pyx_t_8 = __pyx_t_15(__pyx_t_5);
+ if (unlikely(!__pyx_t_8)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_8);
+ }
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
+ __pyx_t_13 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_v_n);
+ __pyx_v_n = __pyx_t_7;
+ __pyx_t_7 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.gettid");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":699
+ * n = 0
+ * for x in referencenames: n += len(x) + 1
+ * header_to_write.target_name = <char**>calloc(n, sizeof(char*)) # <<<<<<<<<<<<<<
+ * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+ * for x from 0 <= x < header_to_write.n_targets:
+ */
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_16, (sizeof(char *))));
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":621
- * return pysam_reference2tid( self.samfile.header, reference )
- *
- * def getrname( self, tid ): # <<<<<<<<<<<<<<
- * '''
- * convert numerical :term:`tid` into :term:`reference` name.'''
+ /* "csamtools.pyx":700
+ * for x in referencenames: n += len(x) + 1
+ * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
+ * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t)) # <<<<<<<<<<<<<<
+ * for x from 0 <= x < header_to_write.n_targets:
+ * header_to_write.target_len[x] = referencelengths[x]
*/
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_16, (sizeof(uint32_t))));
-static PyObject *__pyx_pf_9csamtools_7Samfile_getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getrname");
- __Pyx_TraceCall("getrname", __pyx_f[0], 621);
+ /* "csamtools.pyx":701
+ * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
+ * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+ * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
+ * header_to_write.target_len[x] = referencelengths[x]
+ * name = referencenames[x]
+ */
+ __pyx_t_17 = __pyx_v_header_to_write->n_targets;
+ for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18++) {
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":624
- * '''
- * convert numerical :term:`tid` into :term:`reference` name.'''
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * if not 0 <= tid < self.samfile.header.n_targets:
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ /* "csamtools.pyx":702
+ * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+ * for x from 0 <= x < header_to_write.n_targets:
+ * header_to_write.target_len[x] = referencelengths[x] # <<<<<<<<<<<<<<
+ * name = referencenames[x]
+ * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_19 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_19 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_14 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_14 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_header_to_write->target_len[__pyx_t_14]) = __pyx_t_19;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":625
- * convert numerical :term:`tid` into :term:`reference` name.'''
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
- * return self.samfile.header.target_name[tid]
+ /* "csamtools.pyx":703
+ * for x from 0 <= x < header_to_write.n_targets:
+ * header_to_write.target_len[x] = referencelengths[x]
+ * name = referencenames[x] # <<<<<<<<<<<<<<
+ * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
+ * strncpy( header_to_write.target_name[x], name, len(name) )
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_tid, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
- __Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- }
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_v_name);
+ __pyx_v_name = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":626
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * if not 0 <= tid < self.samfile.header.n_targets:
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
- * return self.samfile.header.target_name[tid]
+ /* "csamtools.pyx":704
+ * header_to_write.target_len[x] = referencelengths[x]
+ * name = referencenames[x]
+ * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char)) # <<<<<<<<<<<<<<
+ * strncpy( header_to_write.target_name[x], name, len(name) )
*
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_tid);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_tid);
- __Pyx_GIVEREF(__pyx_v_tid);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_24), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_14 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_13 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_header_to_write->target_name[__pyx_t_13]) = ((char *)calloc((__pyx_t_14 + 1), (sizeof(char))));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":627
- * if not 0 <= tid < self.samfile.header.n_targets:
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
- * return self.samfile.header.target_name[tid] # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":705
+ * name = referencenames[x]
+ * header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
+ * strncpy( header_to_write.target_name[x], name, len(name) ) # <<<<<<<<<<<<<<
*
- * cdef char * _getrname( self, int tid ):
+ * # Optionally, if there is no text, add a SAM compatible header to output
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_tid); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PyBytes_FromString((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.getrname");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_14 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_14 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_name); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy((__pyx_v_header_to_write->target_name[__pyx_t_14]), __pyx_t_12, __pyx_t_13);
+ __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":629
- * return self.samfile.header.target_name[tid]
- *
- * cdef char * _getrname( self, int tid ): # <<<<<<<<<<<<<<
- * '''
- * convert numerical :term:`tid` into :term:`reference` name.'''
+ /* "csamtools.pyx":701
+ * header_to_write.target_name = <char**>calloc(n, sizeof(char*))
+ * header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+ * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
+ * header_to_write.target_len[x] = referencelengths[x]
+ * name = referencenames[x]
*/
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
-static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, int __pyx_v_tid) {
- char *__pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_getrname");
- __Pyx_TraceCall("_getrname", __pyx_f[0], 629);
+ /* "csamtools.pyx":709
+ * # Optionally, if there is no text, add a SAM compatible header to output
+ * # file.
+ * if text is None and add_sq_text: # <<<<<<<<<<<<<<
+ * text = []
+ * for x from 0 <= x < header_to_write.n_targets:
+ */
+ __pyx_t_1 = (__pyx_v_text == Py_None);
+ if (__pyx_t_1) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_add_sq_text); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __pyx_t_10;
+ } else {
+ __pyx_t_11 = __pyx_t_1;
+ }
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":632
- * '''
- * convert numerical :term:`tid` into :term:`reference` name.'''
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * if not 0 <= tid < self.samfile.header.n_targets:
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ /* "csamtools.pyx":710
+ * # file.
+ * if text is None and add_sq_text:
+ * text = [] # <<<<<<<<<<<<<<
+ * for x from 0 <= x < header_to_write.n_targets:
+ * text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
- }
- __pyx_L3:;
+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_v_text);
+ __pyx_v_text = ((PyObject *)__pyx_t_5);
+ __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":633
- * convert numerical :term:`tid` into :term:`reference` name.'''
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
- * return self.samfile.header.target_name[tid]
+ /* "csamtools.pyx":711
+ * if text is None and add_sq_text:
+ * text = []
+ * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
+ * text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
+ * text = ''.join(text)
*/
- __pyx_t_4 = (0 <= __pyx_v_tid);
- if (__pyx_t_4) {
- __pyx_t_4 = (__pyx_v_tid < __pyx_v_self->samfile->header->n_targets);
- }
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
+ __pyx_t_17 = __pyx_v_header_to_write->n_targets;
+ for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18++) {
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":634
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * if not 0 <= tid < self.samfile.header.n_targets:
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
- * return self.samfile.header.target_name[tid]
+ /* "csamtools.pyx":712
+ * text = []
+ * for x from 0 <= x < header_to_write.n_targets:
+ * text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) ) # <<<<<<<<<<<<<<
+ * text = ''.join(text)
*
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_1 = 0;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_24), __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
- }
- __pyx_L4:;
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_5 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_31), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = __Pyx_PyObject_Append(__pyx_v_text, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":635
- * if not 0 <= tid < self.samfile.header.n_targets:
- * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
- * return self.samfile.header.target_name[tid] # <<<<<<<<<<<<<<
- *
- * def _parseRegion( self,
+ /* "csamtools.pyx":711
+ * if text is None and add_sq_text:
+ * text = []
+ * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
+ * text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
+ * text = ''.join(text)
*/
- __pyx_r = (__pyx_v_self->samfile->header->target_name[__pyx_v_tid]);
- goto __pyx_L0;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_WriteUnraisable("csamtools.Samfile._getrname");
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_8 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":637
- * return self.samfile.header.target_name[tid]
+ /* "csamtools.pyx":713
+ * for x from 0 <= x < header_to_write.n_targets:
+ * text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
+ * text = ''.join(text) # <<<<<<<<<<<<<<
*
- * def _parseRegion( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
+ * if text != None:
*/
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_text);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_text);
+ __Pyx_GIVEREF(__pyx_v_text);
+ __pyx_t_5 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_v_text);
+ __pyx_v_text = __pyx_t_5;
+ __pyx_t_5 = 0;
+ goto __pyx_L24;
+ }
+ __pyx_L24:;
-static PyObject *__pyx_pf_9csamtools_7Samfile__parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile__parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile__parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_reference = 0;
- PyObject *__pyx_v_start = 0;
- PyObject *__pyx_v_end = 0;
- PyObject *__pyx_v_region = 0;
- int __pyx_v_rtid;
- PY_LONG_LONG __pyx_v_rstart;
- PY_LONG_LONG __pyx_v_rend;
- PyObject *__pyx_v_parts;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PY_LONG_LONG __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- Py_ssize_t __pyx_t_9;
- int __pyx_t_10;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_parseRegion");
- __Pyx_TraceCall("_parseRegion", __pyx_f[0], 637);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[4] = {0,0,0,0};
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":638
+ /* "csamtools.pyx":715
+ * text = ''.join(text)
*
- * def _parseRegion( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
+ * if text != None: # <<<<<<<<<<<<<<
+ * # copy without \0
+ * text = _force_bytes(text)
*/
- values[0] = ((PyObject *)Py_None);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_text, Py_None, Py_NE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":639
- * def _parseRegion( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None ):
+ /* "csamtools.pyx":717
+ * if text != None:
+ * # copy without \0
+ * text = _force_bytes(text) # <<<<<<<<<<<<<<
+ * ctext = text
+ * header_to_write.l_text = strlen(ctext)
*/
- values[1] = ((PyObject *)Py_None);
+ __pyx_t_5 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_text)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_v_text);
+ __pyx_v_text = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":640
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None ):
- * '''
+ /* "csamtools.pyx":718
+ * # copy without \0
+ * text = _force_bytes(text)
+ * ctext = text # <<<<<<<<<<<<<<
+ * header_to_write.l_text = strlen(ctext)
+ * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
*/
- values[2] = ((PyObject *)Py_None);
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_ctext = __pyx_t_12;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":641
- * start = None,
- * end = None,
- * region = None ): # <<<<<<<<<<<<<<
- * '''
- * parse region information.
+ /* "csamtools.pyx":719
+ * text = _force_bytes(text)
+ * ctext = text
+ * header_to_write.l_text = strlen(ctext) # <<<<<<<<<<<<<<
+ * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
+ * memcpy( header_to_write.text, ctext, strlen(ctext) )
*/
- values[3] = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (value) { values[0] = value; kw_args--; }
- }
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
- if (value) { values[3] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_reference = values[0];
- __pyx_v_start = values[1];
- __pyx_v_end = values[2];
- __pyx_v_region = values[3];
- } else {
+ __pyx_v_header_to_write->l_text = strlen(__pyx_v_ctext);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":638
+ /* "csamtools.pyx":720
+ * ctext = text
+ * header_to_write.l_text = strlen(ctext)
+ * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) ) # <<<<<<<<<<<<<<
+ * memcpy( header_to_write.text, ctext, strlen(ctext) )
*
- * def _parseRegion( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
*/
- __pyx_v_reference = ((PyObject *)Py_None);
+ __pyx_v_header_to_write->text = ((char *)calloc(strlen(__pyx_v_ctext), (sizeof(char))));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":639
- * def _parseRegion( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None ):
+ /* "csamtools.pyx":721
+ * header_to_write.l_text = strlen(ctext)
+ * header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
+ * memcpy( header_to_write.text, ctext, strlen(ctext) ) # <<<<<<<<<<<<<<
+ *
+ * header_to_write.hash = NULL
*/
- __pyx_v_start = ((PyObject *)Py_None);
+ memcpy(__pyx_v_header_to_write->text, __pyx_v_ctext, strlen(__pyx_v_ctext));
+ goto __pyx_L27;
+ }
+ __pyx_L27:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":640
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None ):
- * '''
+ /* "csamtools.pyx":723
+ * memcpy( header_to_write.text, ctext, strlen(ctext) )
+ *
+ * header_to_write.hash = NULL # <<<<<<<<<<<<<<
+ * header_to_write.rg2lib = NULL
+ *
*/
- __pyx_v_end = ((PyObject *)Py_None);
+ __pyx_v_header_to_write->hash = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":641
- * start = None,
- * end = None,
- * region = None ): # <<<<<<<<<<<<<<
- * '''
- * parse region information.
+ /* "csamtools.pyx":724
+ *
+ * header_to_write.hash = NULL
+ * header_to_write.rg2lib = NULL # <<<<<<<<<<<<<<
+ *
+ * # open file. Header gets written to file at the same time for bam files
*/
- __pyx_v_region = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: __pyx_v_region = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_end = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: __pyx_v_start = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
+ __pyx_v_header_to_write->rg2lib = NULL;
}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_parseRegion", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __Pyx_INCREF(__pyx_v_reference);
- __pyx_v_parts = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L17:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":660
- * cdef long long rend
- *
- * rtid = -1 # <<<<<<<<<<<<<<
- * rstart = 0
- * rend = max_pos
+ /* "csamtools.pyx":728
+ * # open file. Header gets written to file at the same time for bam files
+ * # and sam files (in the latter case, the mode needs to be wh)
+ * store = StderrStore() # <<<<<<<<<<<<<<
+ * self.samfile = samopen( filename, bmode, header_to_write )
+ * store.release()
*/
- __pyx_v_rtid = -1;
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_v_store = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":661
+ /* "csamtools.pyx":729
+ * # and sam files (in the latter case, the mode needs to be wh)
+ * store = StderrStore()
+ * self.samfile = samopen( filename, bmode, header_to_write ) # <<<<<<<<<<<<<<
+ * store.release()
*
- * rtid = -1
- * rstart = 0 # <<<<<<<<<<<<<<
- * rend = max_pos
- * if start != None:
*/
- __pyx_v_rstart = 0;
+ __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":662
- * rtid = -1
- * rstart = 0
- * rend = max_pos # <<<<<<<<<<<<<<
- * if start != None:
- * try:
+ /* "csamtools.pyx":730
+ * store = StderrStore()
+ * self.samfile = samopen( filename, bmode, header_to_write )
+ * store.release() # <<<<<<<<<<<<<<
+ *
+ * # bam_header_destroy takes care of cleaning up of all the members
*/
- __pyx_v_rend = __pyx_v_9csamtools_max_pos;
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":663
- * rstart = 0
- * rend = max_pos
- * if start != None: # <<<<<<<<<<<<<<
- * try:
- * rstart = start
+ /* "csamtools.pyx":733
+ *
+ * # bam_header_destroy takes care of cleaning up of all the members
+ * if not template and header_to_write != NULL: # <<<<<<<<<<<<<<
+ * bam_header_destroy( header_to_write )
+ *
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (!__pyx_t_11);
+ if (__pyx_t_1) {
+ __pyx_t_11 = (__pyx_v_header_to_write != NULL);
+ __pyx_t_10 = __pyx_t_11;
+ } else {
+ __pyx_t_10 = __pyx_t_1;
+ }
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":664
- * rend = max_pos
- * if start != None:
- * try: # <<<<<<<<<<<<<<
- * rstart = start
- * except OverflowError:
+ /* "csamtools.pyx":734
+ * # bam_header_destroy takes care of cleaning up of all the members
+ * if not template and header_to_write != NULL:
+ * bam_header_destroy( header_to_write ) # <<<<<<<<<<<<<<
+ *
+ * elif mode[0] == "r":
*/
- {
- PyObject *__pyx_save_exc_type, *__pyx_save_exc_value, *__pyx_save_exc_tb;
- __Pyx_ExceptionSave(&__pyx_save_exc_type, &__pyx_save_exc_value, &__pyx_save_exc_tb);
- __Pyx_XGOTREF(__pyx_save_exc_type);
- __Pyx_XGOTREF(__pyx_save_exc_value);
- __Pyx_XGOTREF(__pyx_save_exc_tb);
- /*try:*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":665
- * if start != None:
- * try:
- * rstart = start # <<<<<<<<<<<<<<
- * except OverflowError:
- * raise ValueError( 'start out of range (%i)' % start )
- */
- __pyx_t_3 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __pyx_v_rstart = __pyx_t_3;
- }
- __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0;
- __Pyx_XDECREF(__pyx_save_exc_value); __pyx_save_exc_value = 0;
- __Pyx_XDECREF(__pyx_save_exc_tb); __pyx_save_exc_tb = 0;
- goto __pyx_L14_try_end;
- __pyx_L7_error:;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ bam_header_destroy(__pyx_v_header_to_write);
+ goto __pyx_L28;
+ }
+ __pyx_L28:;
+ goto __pyx_L16;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":666
- * try:
- * rstart = start
- * except OverflowError: # <<<<<<<<<<<<<<
- * raise ValueError( 'start out of range (%i)' % start )
+ /* "csamtools.pyx":736
+ * bam_header_destroy( header_to_write )
*
+ * elif mode[0] == "r": # <<<<<<<<<<<<<<
+ * # open file for reading
+ * if strncmp( filename, "-", 1) != 0 and \
*/
- __pyx_t_4 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
- if (__pyx_t_4) {
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion");
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_5, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":667
- * rstart = start
- * except OverflowError:
- * raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":738
+ * elif mode[0] == "r":
+ * # open file for reading
+ * if strncmp( filename, "-", 1) != 0 and \ # <<<<<<<<<<<<<<
+ * not self.isremote and \
+ * not os.path.exists( filename ):
+ */
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = (strncmp(__pyx_t_12, __pyx_k_26, 1) != 0);
+ if (__pyx_t_10) {
+
+ /* "csamtools.pyx":739
+ * # open file for reading
+ * if strncmp( filename, "-", 1) != 0 and \
+ * not self.isremote and \ # <<<<<<<<<<<<<<
+ * not os.path.exists( filename ):
+ * raise IOError( "file `%s` not found" % filename)
+ */
+ __pyx_t_1 = (!__pyx_v_self->isremote);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":740
+ * if strncmp( filename, "-", 1) != 0 and \
+ * not self.isremote and \
+ * not os.path.exists( filename ): # <<<<<<<<<<<<<<
+ * raise IOError( "file `%s` not found" % filename)
*
- * if end != None:
*/
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_start); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
+ __Pyx_GIVEREF(__pyx_v_filename);
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L8_exception_handled;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_21 = (!__pyx_t_11);
+ __pyx_t_11 = __pyx_t_21;
+ } else {
+ __pyx_t_11 = __pyx_t_1;
}
- __pyx_L9_except_error:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- goto __pyx_L1_error;
- __pyx_L8_exception_handled:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- __pyx_L14_try_end:;
+ __pyx_t_1 = __pyx_t_11;
+ } else {
+ __pyx_t_1 = __pyx_t_10;
}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":669
- * raise ValueError( 'start out of range (%i)' % start )
+ /* "csamtools.pyx":741
+ * not self.isremote and \
+ * not os.path.exists( filename ):
+ * raise IOError( "file `%s` not found" % filename) # <<<<<<<<<<<<<<
*
- * if end != None: # <<<<<<<<<<<<<<
- * try:
- * rend = end
+ * # try to detect errors
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_2) {
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L29;
+ }
+ __pyx_L29:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":670
+ /* "csamtools.pyx":744
*
- * if end != None:
- * try: # <<<<<<<<<<<<<<
- * rend = end
- * except OverflowError:
+ * # try to detect errors
+ * self.samfile = samopen( filename, bmode, NULL ) # <<<<<<<<<<<<<<
+ * if self.samfile == NULL:
+ * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
*/
- {
- PyObject *__pyx_save_exc_type, *__pyx_save_exc_value, *__pyx_save_exc_tb;
- __Pyx_ExceptionSave(&__pyx_save_exc_type, &__pyx_save_exc_value, &__pyx_save_exc_tb);
- __Pyx_XGOTREF(__pyx_save_exc_type);
- __Pyx_XGOTREF(__pyx_save_exc_value);
- __Pyx_XGOTREF(__pyx_save_exc_tb);
- /*try:*/ {
+ __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":671
- * if end != None:
- * try:
- * rend = end # <<<<<<<<<<<<<<
- * except OverflowError:
- * raise ValueError( 'end out of range (%i)' % end )
+ /* "csamtools.pyx":745
+ * # try to detect errors
+ * self.samfile = samopen( filename, bmode, NULL )
+ * if self.samfile == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
+ *
*/
- __pyx_t_3 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L18_error;}
- __pyx_v_rend = __pyx_t_3;
- }
- __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0;
- __Pyx_XDECREF(__pyx_save_exc_value); __pyx_save_exc_value = 0;
- __Pyx_XDECREF(__pyx_save_exc_tb); __pyx_save_exc_tb = 0;
- goto __pyx_L25_try_end;
- __pyx_L18_error:;
- __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_1 = (__pyx_v_self->samfile == NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":672
- * try:
- * rend = end
- * except OverflowError: # <<<<<<<<<<<<<<
- * raise ValueError( 'end out of range (%i)' % end )
+ /* "csamtools.pyx":746
+ * self.samfile = samopen( filename, bmode, NULL )
+ * if self.samfile == NULL:
+ * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
*
+ * # bam files require a valid header
*/
- __pyx_t_4 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
- if (__pyx_t_4) {
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion");
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_5, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L30;
+ }
+ __pyx_L30:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":673
- * rend = end
- * except OverflowError:
- * raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":749
*
- * if region:
+ * # bam files require a valid header
+ * if self.isbam: # <<<<<<<<<<<<<<
+ * if self.samfile.header == NULL:
+ * raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
*/
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_10), __pyx_v_end); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ if (__pyx_v_self->isbam) {
+
+ /* "csamtools.pyx":750
+ * # bam files require a valid header
+ * if self.isbam:
+ * if self.samfile.header == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
+ * else:
+ */
+ __pyx_t_1 = (__pyx_v_self->samfile->header == NULL);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":751
+ * if self.isbam:
+ * if self.samfile.header == NULL:
+ * raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) # <<<<<<<<<<<<<<
+ * else:
+ * # in sam files it is optional (samfile full of unmapped reads)
+ */
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L19_exception_handled;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L32;
}
- __pyx_L20_except_error:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- goto __pyx_L1_error;
- __pyx_L19_exception_handled:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- __pyx_L25_try_end:;
+ __pyx_L32:;
+ goto __pyx_L31;
}
- goto __pyx_L17;
- }
- __pyx_L17:;
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":675
- * raise ValueError( 'end out of range (%i)' % end )
+ /* "csamtools.pyx":754
+ * else:
+ * # in sam files it is optional (samfile full of unmapped reads)
+ * if check_header and self.samfile.header == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode )
*
- * if region: # <<<<<<<<<<<<<<
- * parts = re.split( "[:-]", region )
- * reference = parts[0]
*/
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_2) {
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_t_10 = (__pyx_v_self->samfile->header == NULL);
+ __pyx_t_11 = __pyx_t_10;
+ } else {
+ __pyx_t_11 = __pyx_t_1;
+ }
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":676
+ /* "csamtools.pyx":755
+ * # in sam files it is optional (samfile full of unmapped reads)
+ * if check_header and self.samfile.header == NULL:
+ * raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode ) # <<<<<<<<<<<<<<
*
- * if region:
- * parts = re.split( "[:-]", region ) # <<<<<<<<<<<<<<
- * reference = parts[0]
- * if len(parts) >= 2: rstart = int(parts[1]) - 1
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_25));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_25));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
- __Pyx_INCREF(__pyx_v_region);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_region);
- __Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_6 = PyObject_Call(__pyx_t_5, __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_parts);
- __pyx_v_parts = __pyx_t_6;
- __pyx_t_6 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":677
- * if region:
- * parts = re.split( "[:-]", region )
- * reference = parts[0] # <<<<<<<<<<<<<<
- * if len(parts) >= 2: rstart = int(parts[1]) - 1
- * if len(parts) >= 3: rend = int(parts[2])
+ * # disabled for autodetection to work
*/
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_parts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_v_reference);
- __pyx_v_reference = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L33;
+ }
+ __pyx_L33:;
+ }
+ __pyx_L31:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":678
- * parts = re.split( "[:-]", region )
- * reference = parts[0]
- * if len(parts) >= 2: rstart = int(parts[1]) - 1 # <<<<<<<<<<<<<<
- * if len(parts) >= 3: rend = int(parts[2])
+ /* "csamtools.pyx":759
+ * # disabled for autodetection to work
+ * # needs to be disabled so that reading from sam-files without headers works
+ * if check_sq and self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
+ * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
*
*/
- __pyx_t_9 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = (__pyx_t_9 >= 2);
- if (__pyx_t_2) {
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)&PyInt_Type)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_6, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_3 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_v_rstart = __pyx_t_3;
- goto __pyx_L29;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_11) {
+ __pyx_t_1 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_10 = __pyx_t_1;
+ } else {
+ __pyx_t_10 = __pyx_t_11;
}
- __pyx_L29:;
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":679
- * reference = parts[0]
- * if len(parts) >= 2: rstart = int(parts[1]) - 1
- * if len(parts) >= 3: rend = int(parts[2]) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":760
+ * # needs to be disabled so that reading from sam-files without headers works
+ * if check_sq and self.samfile.header.n_targets == 0:
+ * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
*
- * if not reference: return 0, 0, 0, 0
+ * if self.samfile == NULL:
*/
- __pyx_t_9 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = (__pyx_t_9 >= 3);
- if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)&PyInt_Type)), __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_3 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_v_rend = __pyx_t_3;
- goto __pyx_L30;
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L34;
}
- __pyx_L30:;
- goto __pyx_L28;
+ __pyx_L34:;
+ goto __pyx_L16;
}
- __pyx_L28:;
+ __pyx_L16:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":681
- * if len(parts) >= 3: rend = int(parts[2])
+ /* "csamtools.pyx":762
+ * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
*
- * if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
+ * if self.samfile == NULL: # <<<<<<<<<<<<<<
+ * raise IOError("could not open file `%s`" % filename )
*
- * rtid = self.gettid( reference )
*/
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = (!__pyx_t_2);
+ __pyx_t_10 = (__pyx_v_self->samfile == NULL);
if (__pyx_t_10) {
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
- goto __pyx_L31;
- }
- __pyx_L31:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":683
- * if not reference: return 0, 0, 0, 0
+ /* "csamtools.pyx":763
*
- * rtid = self.gettid( reference ) # <<<<<<<<<<<<<<
- * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
- * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
+ * if self.samfile == NULL:
+ * raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
+ *
+ * # check for index and open if present
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_reference);
- __Pyx_GIVEREF(__pyx_v_reference);
- __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_5); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_v_rtid = __pyx_t_4;
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L35;
+ }
+ __pyx_L35:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":684
+ /* "csamtools.pyx":766
*
- * rtid = self.gettid( reference )
- * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) # <<<<<<<<<<<<<<
- * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
- * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
+ * # check for index and open if present
+ * if mode[0] == "r" and self.isbam: # <<<<<<<<<<<<<<
+ *
+ * if not self.isremote:
*/
- __pyx_t_10 = (__pyx_v_rtid < 0);
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_10) {
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_26), __pyx_v_reference); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ __pyx_t_11 = __pyx_v_self->isbam;
+ } else {
+ __pyx_t_11 = __pyx_t_10;
}
- __pyx_L32:;
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":685
- * rtid = self.gettid( reference )
- * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
- * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) # <<<<<<<<<<<<<<
- * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
- * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ /* "csamtools.pyx":768
+ * if mode[0] == "r" and self.isbam:
+ *
+ * if not self.isremote: # <<<<<<<<<<<<<<
+ * if not os.path.exists(filename + b".bai"):
+ * self.index = NULL
*/
- __pyx_t_10 = (__pyx_v_rstart > __pyx_v_rend);
- if (__pyx_t_10) {
- __pyx_t_5 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_27), __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L33;
- }
- __pyx_L33:;
+ __pyx_t_11 = (!__pyx_v_self->isremote);
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":686
- * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
- * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
- * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) # <<<<<<<<<<<<<<
- * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ /* "csamtools.pyx":769
*
+ * if not self.isremote:
+ * if not os.path.exists(filename + b".bai"): # <<<<<<<<<<<<<<
+ * self.index = NULL
+ * else:
*/
- __pyx_t_10 = (0 <= __pyx_v_rstart);
- if (__pyx_t_10) {
- __pyx_t_10 = (__pyx_v_rstart < __pyx_v_9csamtools_max_pos);
- }
- __pyx_t_2 = (!__pyx_t_10);
- if (__pyx_t_2) {
- __pyx_t_6 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L34;
- }
- __pyx_L34:;
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_10 = (!__pyx_t_11);
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":687
- * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
- * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
- * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":770
+ * if not self.isremote:
+ * if not os.path.exists(filename + b".bai"):
+ * self.index = NULL # <<<<<<<<<<<<<<
+ * else:
+ * # returns NULL if there is no index or index could not be opened
+ */
+ __pyx_v_self->index = NULL;
+ goto __pyx_L38;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":773
+ * else:
+ * # returns NULL if there is no index or index could not be opened
+ * self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
+ * if self.index == NULL:
+ * raise IOError("error while opening index `%s` " % filename )
+ */
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->index = bam_index_load(__pyx_t_12);
+
+ /* "csamtools.pyx":774
+ * # returns NULL if there is no index or index could not be opened
+ * self.index = bam_index_load(filename)
+ * if self.index == NULL: # <<<<<<<<<<<<<<
+ * raise IOError("error while opening index `%s` " % filename )
+ * else:
+ */
+ __pyx_t_10 = (__pyx_v_self->index == NULL);
+ if (__pyx_t_10) {
+
+ /* "csamtools.pyx":775
+ * self.index = bam_index_load(filename)
+ * if self.index == NULL:
+ * raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
+ * else:
+ * self.index = bam_index_load(filename)
+ */
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L39;
+ }
+ __pyx_L39:;
+ }
+ __pyx_L38:;
+ goto __pyx_L37;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":777
+ * raise IOError("error while opening index `%s` " % filename )
+ * else:
+ * self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
+ * if self.index == NULL:
+ * raise IOError("error while opening index `%s` " % filename )
+ */
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->index = bam_index_load(__pyx_t_12);
+
+ /* "csamtools.pyx":778
+ * else:
+ * self.index = bam_index_load(filename)
+ * if self.index == NULL: # <<<<<<<<<<<<<<
+ * raise IOError("error while opening index `%s` " % filename )
*
- * return 1, rtid, rstart, rend
*/
- __pyx_t_2 = (0 <= __pyx_v_rend);
- if (__pyx_t_2) {
- __pyx_t_2 = (__pyx_v_rend <= __pyx_v_9csamtools_max_pos);
- }
- __pyx_t_10 = (!__pyx_t_2);
- if (__pyx_t_10) {
- __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_10), __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L35;
- }
- __pyx_L35:;
+ __pyx_t_10 = (__pyx_v_self->index == NULL);
+ if (__pyx_t_10) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":689
- * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ /* "csamtools.pyx":779
+ * self.index = bam_index_load(filename)
+ * if self.index == NULL:
+ * raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
*
- * return 1, rtid, rstart, rend # <<<<<<<<<<<<<<
+ * if not self.isstream:
+ */
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L40;
+ }
+ __pyx_L40:;
+ }
+ __pyx_L37:;
+
+ /* "csamtools.pyx":781
+ * raise IOError("error while opening index `%s` " % filename )
+ *
+ * if not self.isstream: # <<<<<<<<<<<<<<
+ * self.start_offset = bam_tell( self.samfile.x.bam )
*
- * def seek( self, uint64_t offset, int where = 0):
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_int_1);
- __Pyx_GIVEREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_6 = 0;
- __pyx_t_1 = 0;
- __pyx_t_5 = 0;
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L0;
+ __pyx_t_10 = (!__pyx_v_self->isstream);
+ if (__pyx_t_10) {
+
+ /* "csamtools.pyx":782
+ *
+ * if not self.isstream:
+ * self.start_offset = bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
+ *
+ * def gettid( self, reference ):
+ */
+ __pyx_v_self->start_offset = bam_tell(__pyx_v_self->samfile->x.bam);
+ goto __pyx_L41;
+ }
+ __pyx_L41:;
+ goto __pyx_L36;
+ }
+ __pyx_L36:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion");
+ __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_parts);
- __Pyx_DECREF(__pyx_v_reference);
+ __Pyx_XDECREF(__pyx_v_msg);
+ __Pyx_XDECREF(__pyx_v_bmode);
+ __Pyx_XDECREF(__pyx_v_n);
+ __Pyx_XDECREF(__pyx_v_x);
+ __Pyx_XDECREF(__pyx_v_name);
+ __Pyx_XDECREF(__pyx_v_store);
+ __Pyx_XDECREF(__pyx_v_ref);
+ __Pyx_XDECREF(__pyx_v_filename);
+ __Pyx_XDECREF(__pyx_v_referencenames);
+ __Pyx_XDECREF(__pyx_v_text);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":691
- * return 1, rtid, rstart, rend
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_8gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("gettid (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_8gettid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_reference));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":784
+ * self.start_offset = bam_tell( self.samfile.x.bam )
*
- * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
+ * def gettid( self, reference ): # <<<<<<<<<<<<<<
* '''
- * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
+ * convert :term:`reference` name into numerical :term:`tid`
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- uint64_t __pyx_v_offset;
- int __pyx_v_where;
+static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("seek");
- __Pyx_TraceCall("seek", __pyx_f[0], 691);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__where);
- if (value) { values[1] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_offset = __Pyx_PyInt_from_py_uint64_t(values[0]); if (unlikely((__pyx_v_offset == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- if (values[1]) {
- __pyx_v_where = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else {
- __pyx_v_where = ((int)0);
- }
- } else {
- __pyx_v_where = ((int)0);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: __pyx_v_where = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 1: __pyx_v_offset = __Pyx_PyInt_from_py_uint64_t(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((__pyx_v_offset == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.seek");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
+ __Pyx_RefNannySetupContext("gettid", 0);
+ __Pyx_TraceCall("gettid", __pyx_f[0], 784);
+ __Pyx_INCREF(__pyx_v_reference);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":696
+ /* "csamtools.pyx":790
+ * returns -1 if reference is not known.
* '''
- *
- * if not self._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
- * if not self.isbam:
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * reference = _force_bytes(reference)
+ * return pysam_reference2tid( self.samfile.header, reference )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":697
- *
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * if not self.isbam:
- * raise NotImplementedError("seek only available in bam files")
- */
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_39), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":698
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" )
- * if not self.isbam: # <<<<<<<<<<<<<<
- * raise NotImplementedError("seek only available in bam files")
- * return bam_seek( self.samfile.x.bam, offset, where )
- */
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
- if (__pyx_t_4) {
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":699
- * raise ValueError( "I/O operation on closed file" )
- * if not self.isbam:
- * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
- * return bam_seek( self.samfile.x.bam, offset, where )
+ /* "csamtools.pyx":791
+ * '''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * reference = _force_bytes(reference) # <<<<<<<<<<<<<<
+ * return pysam_reference2tid( self.samfile.header, reference )
*
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_28));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_28));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_28));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
- }
- __pyx_L7:;
+ __pyx_t_2 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_reference)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_v_reference);
+ __pyx_v_reference = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":700
- * if not self.isbam:
- * raise NotImplementedError("seek only available in bam files")
- * return bam_seek( self.samfile.x.bam, offset, where ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":792
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * reference = _force_bytes(reference)
+ * return pysam_reference2tid( self.samfile.header, reference ) # <<<<<<<<<<<<<<
*
- * def tell( self ):
+ * def getrname( self, tid ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(__pyx_v_self->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.seek");
+ __Pyx_AddTraceback("csamtools.Samfile.gettid", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_reference);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":702
- * return bam_seek( self.samfile.x.bam, offset, where )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_10getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
+static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("getrname (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_10getrname(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":794
+ * return pysam_reference2tid( self.samfile.header, reference )
*
- * def tell( self ): # <<<<<<<<<<<<<<
+ * def getrname( self, tid ): # <<<<<<<<<<<<<<
* '''
- * return current file position
+ * convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_tell[] = "Samfile.tell(self)\n\n return current file position\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("tell");
- __Pyx_TraceCall("tell", __pyx_f[0], 702);
+ __Pyx_RefNannySetupContext("getrname", 0);
+ __Pyx_TraceCall("getrname", __pyx_f[0], 794);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":706
- * return current file position
+ /* "csamtools.pyx":797
* '''
- * if not self._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
- * if not self.isbam:
+ * convert numerical :term:`tid` into :term:`reference` name.'''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":707
- * '''
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * if not self.isbam:
- * raise NotImplementedError("seek only available in bam files")
- */
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_40), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":708
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" )
- * if not self.isbam: # <<<<<<<<<<<<<<
- * raise NotImplementedError("seek only available in bam files")
- *
+ /* "csamtools.pyx":798
+ * convert numerical :term:`tid` into :term:`reference` name.'''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ * return _charptr_to_str(self.samfile.header.target_name[tid])
*/
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
- if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_RichCompare(__pyx_int_0, __pyx_v_tid, Py_LE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (__Pyx_PyObject_IsTrue(__pyx_t_2)) {
+ __Pyx_DECREF(__pyx_t_2);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ }
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":709
- * raise ValueError( "I/O operation on closed file" )
- * if not self.isbam:
- * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":799
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
+ * return _charptr_to_str(self.samfile.header.target_name[tid])
*
- * return bam_tell( self.samfile.x.bam )
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_tid);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_tid);
+ __Pyx_GIVEREF(__pyx_v_tid);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_28));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_28));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_28));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":711
- * raise NotImplementedError("seek only available in bam files")
- *
- * return bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":800
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ * return _charptr_to_str(self.samfile.header.target_name[tid]) # <<<<<<<<<<<<<<
*
- * def fetch( self,
+ * cdef char * _getrname( self, int tid ): # TODO unused
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_tid); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.tell");
+ __Pyx_AddTraceback("csamtools.Samfile.getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":713
- * return bam_tell( self.samfile.x.bam )
+/* "csamtools.pyx":802
+ * return _charptr_to_str(self.samfile.header.target_name[tid])
*
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
+ * cdef char * _getrname( self, int tid ): # TODO unused # <<<<<<<<<<<<<<
+ * '''
+ * convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can \n be supplied.\n\n Without *reference* or *region* all reads will be fetched. The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n If *until_eof* is given, all reads from the current file position will be returned\n *in order as they are within the file*. \n \n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed \n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_reference = 0;
- PyObject *__pyx_v_start = 0;
- PyObject *__pyx_v_end = 0;
- PyObject *__pyx_v_region = 0;
- PyObject *__pyx_v_callback = 0;
- PyObject *__pyx_v_until_eof = 0;
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- PyObject *__pyx_r = NULL;
+static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, int __pyx_v_tid) {
+ char *__pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
- int __pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
- PyObject *__pyx_t_12 = NULL;
- int __pyx_t_13;
- int __pyx_t_14;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch");
- __Pyx_TraceCall("fetch", __pyx_f[0], 713);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[6] = {0,0,0,0,0,0};
+ __Pyx_RefNannySetupContext("_getrname", 0);
+ __Pyx_TraceCall("_getrname", __pyx_f[0], 802);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":714
- *
- * def fetch( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
+ /* "csamtools.pyx":805
+ * '''
+ * convert numerical :term:`tid` into :term:`reference` name.'''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- values[0] = ((PyObject *)Py_None);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_42), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":715
- * def fetch( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None,
+ /* "csamtools.pyx":806
+ * convert numerical :term:`tid` into :term:`reference` name.'''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ * return self.samfile.header.target_name[tid]
*/
- values[1] = ((PyObject *)Py_None);
+ __pyx_t_4 = (0 <= __pyx_v_tid);
+ if (__pyx_t_4) {
+ __pyx_t_4 = (__pyx_v_tid < __pyx_v_self->samfile->header->n_targets);
+ }
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":716
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None,
- * callback = None,
+ /* "csamtools.pyx":807
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
+ * return self.samfile.header.target_name[tid]
+ *
*/
- values[2] = ((PyObject *)Py_None);
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_2 = 0;
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":717
- * start = None,
- * end = None,
- * region = None, # <<<<<<<<<<<<<<
- * callback = None,
- * until_eof = False ):
+ /* "csamtools.pyx":808
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ * return self.samfile.header.target_name[tid] # <<<<<<<<<<<<<<
+ *
+ * def _parseRegion( self,
*/
- values[3] = ((PyObject *)Py_None);
+ __pyx_r = (__pyx_v_self->samfile->header->target_name[__pyx_v_tid]);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":718
- * end = None,
- * region = None,
- * callback = None, # <<<<<<<<<<<<<<
- * until_eof = False ):
- * '''
- */
- values[4] = ((PyObject *)Py_None);
- values[5] = __pyx_k_29;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
- case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (value) { values[0] = value; kw_args--; }
- }
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
- if (value) { values[3] = value; kw_args--; }
- }
- case 4:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__callback);
- if (value) { values[4] = value; kw_args--; }
- }
- case 5:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__until_eof);
- if (value) { values[5] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_reference = values[0];
- __pyx_v_start = values[1];
- __pyx_v_end = values[2];
- __pyx_v_region = values[3];
- __pyx_v_callback = values[4];
- __pyx_v_until_eof = values[5];
- } else {
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_WriteUnraisable("csamtools.Samfile._getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":714
- *
- * def fetch( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
- */
- __pyx_v_reference = ((PyObject *)Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_12_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_reference = 0;
+ PyObject *__pyx_v_start = 0;
+ PyObject *__pyx_v_end = 0;
+ PyObject *__pyx_v_region = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_parseRegion (wrapper)", 0);
+ {
+ PyObject* values[4] = {0,0,0,0};
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":715
- * def fetch( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None,
+ /* "csamtools.pyx":811
+ *
+ * def _parseRegion( self,
+ * reference = None, # <<<<<<<<<<<<<<
+ * start = None,
+ * end = None,
*/
- __pyx_v_start = ((PyObject *)Py_None);
+ values[0] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":716
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None,
- * callback = None,
+ /* "csamtools.pyx":812
+ * def _parseRegion( self,
+ * reference = None,
+ * start = None, # <<<<<<<<<<<<<<
+ * end = None,
+ * region = None ):
*/
- __pyx_v_end = ((PyObject *)Py_None);
+ values[1] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":717
- * start = None,
- * end = None,
- * region = None, # <<<<<<<<<<<<<<
- * callback = None,
- * until_eof = False ):
+ /* "csamtools.pyx":813
+ * reference = None,
+ * start = None,
+ * end = None, # <<<<<<<<<<<<<<
+ * region = None ):
+ * '''
*/
- __pyx_v_region = ((PyObject *)Py_None);
+ values[2] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":718
- * end = None,
- * region = None,
- * callback = None, # <<<<<<<<<<<<<<
- * until_eof = False ):
+ /* "csamtools.pyx":814
+ * start = None,
+ * end = None,
+ * region = None ): # <<<<<<<<<<<<<<
* '''
+ * parse region information.
*/
- __pyx_v_callback = ((PyObject *)Py_None);
- __pyx_v_until_eof = __pyx_k_29;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 6: __pyx_v_until_eof = PyTuple_GET_ITEM(__pyx_args, 5);
- case 5: __pyx_v_callback = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: __pyx_v_region = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_end = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: __pyx_v_start = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
+ values[3] = ((PyObject *)Py_None);
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
+ if (value) { values[0] = value; kw_args--; }
+ }
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
}
+ __pyx_v_reference = values[0];
+ __pyx_v_start = values[1];
+ __pyx_v_end = values[2];
+ __pyx_v_region = values[3];
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parseRegion", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.fetch");
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_12_parseRegion(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":742
- * cdef int rtid, rstart, rend, has_coord
- *
- * if not self._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
+/* "csamtools.pyx":810
+ * return self.samfile.header.target_name[tid]
*
+ * def _parseRegion( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":743
- *
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
+ int __pyx_v_rtid;
+ PY_LONG_LONG __pyx_v_rstart;
+ PY_LONG_LONG __pyx_v_rend;
+ PyObject *__pyx_v_parts = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PY_LONG_LONG __pyx_t_6;
+ int __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_parseRegion", 0);
+ __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810);
+ __Pyx_INCREF(__pyx_v_reference);
+ __Pyx_INCREF(__pyx_v_region);
+
+ /* "csamtools.pyx":833
+ * cdef long long rend
*
- * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ * rtid = -1 # <<<<<<<<<<<<<<
+ * rstart = 0
+ * rend = max_pos
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_v_rtid = -1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":745
- * raise ValueError( "I/O operation on closed file" )
- *
- * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":834
*
- * if self.isbam:
+ * rtid = -1
+ * rstart = 0 # <<<<<<<<<<<<<<
+ * rend = max_pos
+ * if start != None:
+ */
+ __pyx_v_rstart = 0;
+
+ /* "csamtools.pyx":835
+ * rtid = -1
+ * rstart = 0
+ * rend = max_pos # <<<<<<<<<<<<<<
+ * if start != None:
+ * try:
+ */
+ __pyx_v_rend = __pyx_v_9csamtools_max_pos;
+
+ /* "csamtools.pyx":836
+ * rstart = 0
+ * rend = max_pos
+ * if start != None: # <<<<<<<<<<<<<<
+ * try:
+ * rstart = start
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
- __Pyx_GIVEREF(__pyx_v_reference);
- __Pyx_INCREF(__pyx_v_start);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_start);
- __Pyx_GIVEREF(__pyx_v_start);
- __Pyx_INCREF(__pyx_v_end);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end);
- __Pyx_GIVEREF(__pyx_v_end);
- __Pyx_INCREF(__pyx_v_region);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_v_region);
- __Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyTuple_CheckExact(__pyx_t_5) && likely(PyTuple_GET_SIZE(__pyx_t_5) == 4)) {
- PyObject* tuple = __pyx_t_5;
- __pyx_t_2 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_2);
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_1 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_1);
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = PyTuple_GET_ITEM(tuple, 2); __Pyx_INCREF(__pyx_t_6);
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = PyTuple_GET_ITEM(tuple, 3); __Pyx_INCREF(__pyx_t_7);
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_v_has_coord = __pyx_t_8;
- __pyx_v_rtid = __pyx_t_9;
- __pyx_v_rstart = __pyx_t_10;
- __pyx_v_rend = __pyx_t_11;
- } else {
- __pyx_t_12 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_2 = __Pyx_UnpackItem(__pyx_t_12, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_1 = __Pyx_UnpackItem(__pyx_t_12, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = __Pyx_UnpackItem(__pyx_t_12, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __Pyx_UnpackItem(__pyx_t_12, 3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__Pyx_EndUnpack(__pyx_t_12, 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_v_has_coord = __pyx_t_11;
- __pyx_v_rtid = __pyx_t_10;
- __pyx_v_rstart = __pyx_t_9;
- __pyx_v_rend = __pyx_t_8;
- }
+ if (__pyx_t_2) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":747
- * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
- *
- * if self.isbam: # <<<<<<<<<<<<<<
- * if not until_eof and not self._hasIndex() and not self.isremote:
- * raise ValueError( "fetch called on bamfile without index" )
+ /* "csamtools.pyx":837
+ * rend = max_pos
+ * if start != None:
+ * try: # <<<<<<<<<<<<<<
+ * rstart = start
+ * except OverflowError:
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_3, &__pyx_t_4, &__pyx_t_5);
+ __Pyx_XGOTREF(__pyx_t_3);
+ __Pyx_XGOTREF(__pyx_t_4);
+ __Pyx_XGOTREF(__pyx_t_5);
+ /*try:*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":748
- *
- * if self.isbam:
- * if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
- * raise ValueError( "fetch called on bamfile without index" )
- *
+ /* "csamtools.pyx":838
+ * if start != None:
+ * try:
+ * rstart = start # <<<<<<<<<<<<<<
+ * except OverflowError:
+ * raise ValueError( 'start out of range (%i)' % start )
*/
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_13 = (!__pyx_t_4);
- if (__pyx_t_13) {
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
- __pyx_t_14 = __pyx_t_4;
- } else {
- __pyx_t_14 = __pyx_t_13;
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_v_rstart = __pyx_t_6;
}
- __pyx_t_13 = __pyx_t_14;
- } else {
- __pyx_t_13 = __pyx_t_3;
- }
- if (__pyx_t_13) {
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
+ goto __pyx_L11_try_end;
+ __pyx_L4_error:;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":749
- * if self.isbam:
- * if not until_eof and not self._hasIndex() and not self.isremote:
- * raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":839
+ * try:
+ * rstart = start
+ * except OverflowError: # <<<<<<<<<<<<<<
+ * raise ValueError( 'start out of range (%i)' % start )
*
- * if callback:
*/
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_30));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_kp_s_30));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_30));
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
- }
- __pyx_L8:;
+ __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
+ if (__pyx_t_7) {
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_9);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":751
- * raise ValueError( "fetch called on bamfile without index" )
+ /* "csamtools.pyx":840
+ * rstart = start
+ * except OverflowError:
+ * raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
*
- * if callback: # <<<<<<<<<<<<<<
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * if end != None:
*/
- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_13) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":752
- *
- * if callback:
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
- * return bam_fetch(self.samfile.x.bam,
- */
- __pyx_t_13 = (!__pyx_v_has_coord);
- if (__pyx_t_13) {
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_31));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_31));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_31));
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
- }
- __pyx_L10:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":753
- * if callback:
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
- * return bam_fetch(self.samfile.x.bam,
- * self.index,
- */
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_3 = (!__pyx_t_13);
- if (__pyx_t_3) {
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
+ __Pyx_Raise(__pyx_t_10, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ goto __pyx_L5_exception_handled;
}
- __pyx_L11:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":754
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
- * return bam_fetch(self.samfile.x.bam, # <<<<<<<<<<<<<<
- * self.index,
- * rtid,
- */
- __Pyx_XDECREF(__pyx_r);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":760
- * rend,
- * <void*>callback,
- * fetch_callback ) # <<<<<<<<<<<<<<
- * else:
- * if has_coord:
- */
- __pyx_t_7 = PyInt_FromLong(bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L0;
- goto __pyx_L9;
+ __pyx_L6_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_XGIVEREF(__pyx_t_5);
+ __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
+ goto __pyx_L1_error;
+ __pyx_L5_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_XGIVEREF(__pyx_t_5);
+ __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
+ __pyx_L11_try_end:;
}
- /*else*/ {
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":762
- * fetch_callback )
- * else:
- * if has_coord: # <<<<<<<<<<<<<<
- * return IteratorRowRegion( self, rtid, rstart, rend )
- * else:
+ /* "csamtools.pyx":842
+ * raise ValueError( 'start out of range (%i)' % start )
+ *
+ * if end != None: # <<<<<<<<<<<<<<
+ * try:
+ * rend = end
*/
- if (__pyx_v_has_coord) {
+ __pyx_t_9 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ if (__pyx_t_2) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":763
- * else:
- * if has_coord:
- * return IteratorRowRegion( self, rtid, rstart, rend ) # <<<<<<<<<<<<<<
- * else:
- * if until_eof:
+ /* "csamtools.pyx":843
+ *
+ * if end != None:
+ * try: # <<<<<<<<<<<<<<
+ * rend = end
+ * except OverflowError:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_7 = 0;
- __pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L0;
- goto __pyx_L12;
- }
- /*else*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_5, &__pyx_t_4, &__pyx_t_3);
+ __Pyx_XGOTREF(__pyx_t_5);
+ __Pyx_XGOTREF(__pyx_t_4);
+ __Pyx_XGOTREF(__pyx_t_3);
+ /*try:*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":765
- * return IteratorRowRegion( self, rtid, rstart, rend )
- * else:
- * if until_eof: # <<<<<<<<<<<<<<
- * return IteratorRowAll( self )
- * else:
+ /* "csamtools.pyx":844
+ * if end != None:
+ * try:
+ * rend = end # <<<<<<<<<<<<<<
+ * except OverflowError:
+ * raise ValueError( 'end out of range (%i)' % end )
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 765; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_3) {
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_v_rend = __pyx_t_6;
+ }
+ __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L22_try_end;
+ __pyx_L15_error:;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":766
- * else:
- * if until_eof:
- * return IteratorRowAll( self ) # <<<<<<<<<<<<<<
- * else:
- * return IteratorRowAllRefs(self)
+ /* "csamtools.pyx":845
+ * try:
+ * rend = end
+ * except OverflowError: # <<<<<<<<<<<<<<
+ * raise ValueError( 'end out of range (%i)' % end )
+ *
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
- goto __pyx_L13;
- }
- /*else*/ {
+ __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
+ if (__pyx_t_7) {
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_1);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":768
- * return IteratorRowAll( self )
- * else:
- * return IteratorRowAllRefs(self) # <<<<<<<<<<<<<<
- * else:
- * # check if header is present - otherwise sam_read1 aborts
+ /* "csamtools.pyx":846
+ * rend = end
+ * except OverflowError:
+ * raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
+ *
+ * if region:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAllRefs)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L0;
- }
- __pyx_L13:;
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
+ __Pyx_Raise(__pyx_t_10, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L16_exception_handled;
}
- __pyx_L12:;
+ __pyx_L17_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_5);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
+ goto __pyx_L1_error;
+ __pyx_L16_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_5);
+ __Pyx_XGIVEREF(__pyx_t_4);
+ __Pyx_XGIVEREF(__pyx_t_3);
+ __Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
+ __pyx_L22_try_end:;
}
- __pyx_L9:;
- goto __pyx_L7;
+ goto __pyx_L14;
}
- /*else*/ {
+ __pyx_L14:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":772
- * # check if header is present - otherwise sam_read1 aborts
- * # this happens if a bamfile is opened with mode 'r'
- * if self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
- * raise ValueError( "fetch called for samfile without header")
+ /* "csamtools.pyx":848
+ * raise ValueError( 'end out of range (%i)' % end )
*
+ * if region: # <<<<<<<<<<<<<<
+ * region = _force_str(region)
+ * parts = re.split( "[:-]", region )
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
- if (__pyx_t_3) {
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_2) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":773
- * # this happens if a bamfile is opened with mode 'r'
- * if self.samfile.header.n_targets == 0:
- * raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":849
*
- * if region != None:
+ * if region:
+ * region = _force_str(region) # <<<<<<<<<<<<<<
+ * parts = re.split( "[:-]", region )
+ * reference = parts[0]
*/
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_33));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_kp_s_33));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_33));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
- }
- __pyx_L14:;
+ __pyx_t_1 = __pyx_f_9csamtools__force_str(__pyx_v_region); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_v_region);
+ __pyx_v_region = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":775
- * raise ValueError( "fetch called for samfile without header")
- *
- * if region != None: # <<<<<<<<<<<<<<
- * raise ValueError ("fetch for a region is not available for sam files" )
- * if callback:
+ /* "csamtools.pyx":850
+ * if region:
+ * region = _force_str(region)
+ * parts = re.split( "[:-]", region ) # <<<<<<<<<<<<<<
+ * reference = parts[0]
+ * if len(parts) >= 2: rstart = int(parts[1]) - 1
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_region, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_3) {
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_43));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
+ __Pyx_INCREF(__pyx_v_region);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_region);
+ __Pyx_GIVEREF(__pyx_v_region);
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_v_parts = __pyx_t_9;
+ __pyx_t_9 = 0;
+
+ /* "csamtools.pyx":851
+ * region = _force_str(region)
+ * parts = re.split( "[:-]", region )
+ * reference = parts[0] # <<<<<<<<<<<<<<
+ * if len(parts) >= 2: rstart = int(parts[1]) - 1
+ * if len(parts) >= 3: rend = int(parts[2])
+ */
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_v_reference);
+ __pyx_v_reference = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":776
+ /* "csamtools.pyx":852
+ * parts = re.split( "[:-]", region )
+ * reference = parts[0]
+ * if len(parts) >= 2: rstart = int(parts[1]) - 1 # <<<<<<<<<<<<<<
+ * if len(parts) >= 3: rend = int(parts[2])
*
- * if region != None:
- * raise ValueError ("fetch for a region is not available for sam files" ) # <<<<<<<<<<<<<<
- * if callback:
- * raise NotImplementedError( "callback not implemented yet" )
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = (__pyx_t_12 >= 2);
+ if (__pyx_t_2) {
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_34));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_34));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_34));
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
+ __pyx_v_rstart = __pyx_t_6;
+ goto __pyx_L26;
}
- __pyx_L15:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":777
- * if region != None:
- * raise ValueError ("fetch for a region is not available for sam files" )
- * if callback: # <<<<<<<<<<<<<<
- * raise NotImplementedError( "callback not implemented yet" )
- * else:
- */
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_3) {
+ __pyx_L26:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":778
- * raise ValueError ("fetch for a region is not available for sam files" )
- * if callback:
- * raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
- * else:
- * return IteratorRowAll( self )
+ /* "csamtools.pyx":853
+ * reference = parts[0]
+ * if len(parts) >= 2: rstart = int(parts[1]) - 1
+ * if len(parts) >= 3: rend = int(parts[2]) # <<<<<<<<<<<<<<
+ *
+ * if not reference: return 0, 0, 0, 0
*/
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_35));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_kp_s_35));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = (__pyx_t_12 >= 3);
+ if (__pyx_t_2) {
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ __pyx_v_rend = __pyx_t_6;
+ goto __pyx_L27;
}
- /*else*/ {
+ __pyx_L27:;
+ goto __pyx_L25;
+ }
+ __pyx_L25:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":780
- * raise NotImplementedError( "callback not implemented yet" )
- * else:
- * return IteratorRowAll( self ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":855
+ * if len(parts) >= 3: rend = int(parts[2])
*
- * def mate( self,
+ * if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
+ *
+ * rtid = self.gettid( reference )
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L0;
- }
- __pyx_L16:;
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = (!__pyx_t_2);
+ if (__pyx_t_13) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_k_tuple_44));
+ __pyx_r = ((PyObject *)__pyx_k_tuple_44);
+ goto __pyx_L0;
+ goto __pyx_L28;
}
- __pyx_L7:;
+ __pyx_L28:;
+
+ /* "csamtools.pyx":857
+ * if not reference: return 0, 0, 0, 0
+ *
+ * rtid = self.gettid( reference ) # <<<<<<<<<<<<<<
+ * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
+ * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
+ */
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_v_reference);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_reference);
+ __Pyx_GIVEREF(__pyx_v_reference);
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_7 = __Pyx_PyInt_AsInt(__pyx_t_8); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_rtid = __pyx_t_7;
+
+ /* "csamtools.pyx":858
+ *
+ * rtid = self.gettid( reference )
+ * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) # <<<<<<<<<<<<<<
+ * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
+ * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
+ */
+ __pyx_t_13 = (__pyx_v_rtid < 0);
+ if (__pyx_t_13) {
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L29;
+ }
+ __pyx_L29:;
+
+ /* "csamtools.pyx":859
+ * rtid = self.gettid( reference )
+ * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
+ * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) # <<<<<<<<<<<<<<
+ * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
+ * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ */
+ __pyx_t_13 = (__pyx_v_rstart > __pyx_v_rend);
+ if (__pyx_t_13) {
+ __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_8 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_46), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_Raise(__pyx_t_9, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L30;
+ }
+ __pyx_L30:;
+
+ /* "csamtools.pyx":860
+ * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
+ * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
+ * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) # <<<<<<<<<<<<<<
+ * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ *
+ */
+ __pyx_t_13 = (0 <= __pyx_v_rstart);
+ if (__pyx_t_13) {
+ __pyx_t_13 = (__pyx_v_rstart < __pyx_v_9csamtools_max_pos);
+ }
+ __pyx_t_2 = (!__pyx_t_13);
+ if (__pyx_t_2) {
+ __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L31;
+ }
+ __pyx_L31:;
+
+ /* "csamtools.pyx":861
+ * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
+ * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
+ * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend ) # <<<<<<<<<<<<<<
+ *
+ * return 1, rtid, rstart, rend
+ */
+ __pyx_t_2 = (0 <= __pyx_v_rend);
+ if (__pyx_t_2) {
+ __pyx_t_2 = (__pyx_v_rend <= __pyx_v_9csamtools_max_pos);
+ }
+ __pyx_t_13 = (!__pyx_t_2);
+ if (__pyx_t_13) {
+ __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_Raise(__pyx_t_9, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L32;
+ }
+ __pyx_L32:;
+
+ /* "csamtools.pyx":863
+ * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ *
+ * return 1, rtid, rstart, rend # <<<<<<<<<<<<<<
+ *
+ * def reset( self ):
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_9 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_INCREF(__pyx_int_1);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_int_1);
+ __Pyx_GIVEREF(__pyx_int_1);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_9 = 0;
+ __pyx_t_1 = 0;
+ __pyx_t_8 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_10);
+ __pyx_t_10 = 0;
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_12);
- __Pyx_AddTraceback("csamtools.Samfile.fetch");
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_parts);
+ __Pyx_XDECREF(__pyx_v_reference);
+ __Pyx_XDECREF(__pyx_v_region);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":782
- * return IteratorRowAll( self )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_14reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
+static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("reset (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_14reset(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":865
+ * return 1, rtid, rstart, rend
*
- * def mate( self, # <<<<<<<<<<<<<<
- * AlignedRead read ):
- * '''return the mate of :class:`AlignedRead` *read*.
+ * def reset( self ): # <<<<<<<<<<<<<<
+ * '''reset file position to beginning of read section.'''
+ * return self.seek( self.start_offset, 0 )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
- uint32_t __pyx_v_flag;
- __pyx_t_9csamtools_MateData __pyx_v_mate_data;
- int __pyx_v_x;
- struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
+static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- int __pyx_t_1;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate");
- __Pyx_TraceCall("mate", __pyx_f[0], 782);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_TraceCall("reset", __pyx_f[0], 865);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":795
+ /* "csamtools.pyx":867
+ * def reset( self ):
+ * '''reset file position to beginning of read section.'''
+ * return self.seek( self.start_offset, 0 ) # <<<<<<<<<<<<<<
*
- * '''
- * cdef uint32_t flag = read._delegate.core.flag # <<<<<<<<<<<<<<
+ * def seek( self, uint64_t offset, int where = 0):
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.Samfile.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_16seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ uint64_t __pyx_v_offset;
+ int __pyx_v_where;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("seek (wrapper)", 0);
+ {
+ PyObject* values[2] = {0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__where);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ if (values[1]) {
+ } else {
+ __pyx_v_where = ((int)0);
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_offset = __Pyx_PyInt_from_py_uint64_t(values[0]); if (unlikely((__pyx_v_offset == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (values[1]) {
+ __pyx_v_where = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_where = ((int)0);
+ }
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_16seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_offset, __pyx_v_where);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":869
+ * return self.seek( self.start_offset, 0 )
*
- * if flag & BAM_FPAIRED == 0:
+ * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
+ * '''
+ * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
*/
- __pyx_v_flag = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.flag;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":797
- * cdef uint32_t flag = read._delegate.core.flag
+static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("seek", 0);
+ __Pyx_TraceCall("seek", __pyx_f[0], 869);
+
+ /* "csamtools.pyx":874
+ * '''
*
- * if flag & BAM_FPAIRED == 0: # <<<<<<<<<<<<<<
- * raise ValueError( "read %s: is unpaired" % (read.qname))
- * if flag & BAM_FMUNMAP != 0:
+ * if not self._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam:
*/
- __pyx_t_1 = ((__pyx_v_flag & 1) == 0);
- if (__pyx_t_1) {
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":798
+ /* "csamtools.pyx":875
*
- * if flag & BAM_FPAIRED == 0:
- * raise ValueError( "read %s: is unpaired" % (read.qname)) # <<<<<<<<<<<<<<
- * if flag & BAM_FMUNMAP != 0:
- * raise ValueError( "mate %s: is unmapped" % (read.qname))
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files")
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":799
- * if flag & BAM_FPAIRED == 0:
- * raise ValueError( "read %s: is unpaired" % (read.qname))
- * if flag & BAM_FMUNMAP != 0: # <<<<<<<<<<<<<<
- * raise ValueError( "mate %s: is unmapped" % (read.qname))
- *
+ /* "csamtools.pyx":876
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: # <<<<<<<<<<<<<<
+ * raise NotImplementedError("seek only available in bam files")
+ * if self.isstream:
*/
- __pyx_t_1 = ((__pyx_v_flag & 8) != 0);
- if (__pyx_t_1) {
+ __pyx_t_4 = (!__pyx_v_self->isbam);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":800
- * raise ValueError( "read %s: is unpaired" % (read.qname))
- * if flag & BAM_FMUNMAP != 0:
- * raise ValueError( "mate %s: is unmapped" % (read.qname)) # <<<<<<<<<<<<<<
- *
- * cdef MateData mate_data
+ /* "csamtools.pyx":877
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
+ * if self.isstream:
+ * raise OSError("seek no available in streams")
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_37), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_49), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":804
- * cdef MateData mate_data
+ /* "csamtools.pyx":878
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files")
+ * if self.isstream: # <<<<<<<<<<<<<<
+ * raise OSError("seek no available in streams")
*
- * mate_data.name = <char *>bam1_qname(read._delegate) # <<<<<<<<<<<<<<
- * mate_data.mate = NULL
- * # xor flags to get the other mate
*/
- __pyx_v_mate_data.name = bam1_qname(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate);
+ if (__pyx_v_self->isstream) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":805
+ /* "csamtools.pyx":879
+ * raise NotImplementedError("seek only available in bam files")
+ * if self.isstream:
+ * raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
*
- * mate_data.name = <char *>bam1_qname(read._delegate)
- * mate_data.mate = NULL # <<<<<<<<<<<<<<
- * # xor flags to get the other mate
- * cdef int x = BAM_FREAD1 + BAM_FREAD2
+ * return bam_seek( self.samfile.x.bam, offset, where )
*/
- __pyx_v_mate_data.mate = NULL;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_OSError, ((PyObject *)__pyx_k_tuple_51), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":807
- * mate_data.mate = NULL
- * # xor flags to get the other mate
- * cdef int x = BAM_FREAD1 + BAM_FREAD2 # <<<<<<<<<<<<<<
- * mate_data.flag = ( flag ^ x) & x
+ /* "csamtools.pyx":881
+ * raise OSError("seek no available in streams")
*
- */
- __pyx_v_x = 192;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":808
- * # xor flags to get the other mate
- * cdef int x = BAM_FREAD1 + BAM_FREAD2
- * mate_data.flag = ( flag ^ x) & x # <<<<<<<<<<<<<<
+ * return bam_seek( self.samfile.x.bam, offset, where ) # <<<<<<<<<<<<<<
*
- * bam_fetch(self.samfile.x.bam,
+ * def tell( self ):
*/
- __pyx_v_mate_data.flag = ((__pyx_v_flag ^ __pyx_v_x) & __pyx_v_x);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(__pyx_v_self->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":816
- * read._delegate.core.mpos + 1,
- * <void*>&mate_data,
- * mate_callback ) # <<<<<<<<<<<<<<
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_18tell[] = "Samfile.tell(self)\n\n return current file position\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("tell (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_18tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":883
+ * return bam_seek( self.samfile.x.bam, offset, where )
*
- * if mate_data.mate == NULL:
+ * def tell( self ): # <<<<<<<<<<<<<<
+ * '''
+ * return current file position
*/
- bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mtid, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos, (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":818
- * mate_callback )
- *
- * if mate_data.mate == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "mate not found" )
- *
+static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("tell", 0);
+ __Pyx_TraceCall("tell", __pyx_f[0], 883);
+
+ /* "csamtools.pyx":887
+ * return current file position
+ * '''
+ * if not self._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam:
*/
- __pyx_t_1 = (__pyx_v_mate_data.mate == NULL);
- if (__pyx_t_1) {
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":819
- *
- * if mate_data.mate == NULL:
- * raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
- *
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
+ /* "csamtools.pyx":888
+ * '''
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files")
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_52), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_38));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_38));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_38));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L7:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":821
- * raise ValueError( "mate not found" )
+ /* "csamtools.pyx":889
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: # <<<<<<<<<<<<<<
+ * raise NotImplementedError("seek only available in bam files")
*
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
- * dest._delegate = mate_data.mate
- * return dest
*/
- __pyx_t_3 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (!(likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = (!__pyx_v_self->isbam);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":822
- *
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
- * dest._delegate = mate_data.mate # <<<<<<<<<<<<<<
- * return dest
+ /* "csamtools.pyx":890
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
*
+ * return bam_tell( self.samfile.x.bam )
*/
- __pyx_v_dest->_delegate = __pyx_v_mate_data.mate;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_53), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":823
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
- * dest._delegate = mate_data.mate
- * return dest # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":892
+ * raise NotImplementedError("seek only available in bam files")
*
- * def count( self,
+ * return bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
+ *
+ * def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_dest));
- __pyx_r = ((PyObject *)__pyx_v_dest);
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(__pyx_v_self->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Samfile.mate");
+ __Pyx_AddTraceback("csamtools.Samfile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":825
- * return dest
- *
- * def count( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n \n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_20fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n\n If *until_eof* is given, all reads from the current file position will be returned\n in order as they are within the file. Using this option will also fetch unmapped reads.\n\n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed\n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
+ PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_until_eof = 0;
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_counter;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
- int __pyx_t_9;
- int __pyx_t_10;
- PyObject *__pyx_t_11 = NULL;
- int __pyx_t_12;
- int __pyx_t_13;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count");
- __Pyx_TraceCall("count", __pyx_f[0], 825);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[5] = {0,0,0,0,0};
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ {
+ PyObject* values[6] = {0,0,0,0,0,0};
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":826
+ /* "csamtools.pyx":895
*
- * def count( self,
+ * def fetch( self,
* reference = None, # <<<<<<<<<<<<<<
* start = None,
* end = None,
*/
values[0] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":827
- * def count( self,
+ /* "csamtools.pyx":896
+ * def fetch( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
* end = None,
*/
values[1] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":828
+ /* "csamtools.pyx":897
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
* region = None,
- * until_eof = False ):
+ * callback = None,
*/
values[2] = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":829
+ /* "csamtools.pyx":898
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
+ * callback = None,
* until_eof = False ):
- * '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
*/
values[3] = ((PyObject *)Py_None);
- values[4] = __pyx_k_39;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (value) { values[0] = value; kw_args--; }
- }
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (value) { values[1] = value; kw_args--; }
+
+ /* "csamtools.pyx":899
+ * end = None,
+ * region = None,
+ * callback = None, # <<<<<<<<<<<<<<
+ * until_eof = False ):
+ * '''
+ */
+ values[4] = ((PyObject *)Py_None);
+ values[5] = __pyx_k_54;
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
}
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (value) { values[2] = value; kw_args--; }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
+ if (value) { values[0] = value; kw_args--; }
+ }
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__callback);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ case 5:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__until_eof);
+ if (value) { values[5] = value; kw_args--; }
+ }
}
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
- if (value) { values[3] = value; kw_args--; }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
- case 4:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__until_eof);
- if (value) { values[4] = value; kw_args--; }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
}
}
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
__pyx_v_reference = values[0];
__pyx_v_start = values[1];
__pyx_v_end = values[2];
__pyx_v_region = values[3];
- __pyx_v_until_eof = values[4];
- } else {
+ __pyx_v_callback = values[4];
+ __pyx_v_until_eof = values[5];
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_20fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_until_eof);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":826
+/* "csamtools.pyx":894
+ * return bam_tell( self.samfile.x.bam )
*
- * def count( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
- */
- __pyx_v_reference = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":827
- * def count( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None,
- */
- __pyx_v_start = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":828
+ * def fetch( self, # <<<<<<<<<<<<<<
* reference = None,
* start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None,
- * until_eof = False ):
*/
- __pyx_v_end = ((PyObject *)Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":829
- * start = None,
- * end = None,
- * region = None, # <<<<<<<<<<<<<<
- * until_eof = False ):
- * '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
- */
- __pyx_v_region = ((PyObject *)Py_None);
- __pyx_v_until_eof = __pyx_k_39;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 5: __pyx_v_until_eof = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: __pyx_v_region = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_end = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: __pyx_v_start = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("count", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.count");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __Pyx_INCREF(__pyx_v_region);
+static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof) {
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ int __pyx_v_reopen;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_t_15;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch", 0);
+ __Pyx_TraceCall("fetch", __pyx_f[0], 894);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":843
- * cdef int rend
+ /* "csamtools.pyx":924
+ * cdef int rtid, rstart, rend, has_coord
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":844
+ /* "csamtools.pyx":925
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
- * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_55), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":846
+ /* "csamtools.pyx":927
* raise ValueError( "I/O operation on closed file" )
*
- * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
- * cdef int counter
+ * if self.isstream: reopen = False
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
__Pyx_INCREF(__pyx_v_start);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_start);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_start);
__Pyx_GIVEREF(__pyx_v_start);
__Pyx_INCREF(__pyx_v_end);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_end);
__Pyx_GIVEREF(__pyx_v_end);
__Pyx_INCREF(__pyx_v_region);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_v_region);
+ PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyTuple_CheckExact(__pyx_t_5) && likely(PyTuple_GET_SIZE(__pyx_t_5) == 4)) {
- PyObject* tuple = __pyx_t_5;
- __pyx_t_2 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_1);
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = PyTuple_GET_ITEM(tuple, 2); __Pyx_INCREF(__pyx_t_6);
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = PyTuple_GET_ITEM(tuple, 3); __Pyx_INCREF(__pyx_t_7);
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
+ PyObject* sequence = __pyx_t_5;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+ if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+ if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_6 = PyList_GET_ITEM(sequence, 2);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 3);
+ }
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_v_region);
- __pyx_v_region = __pyx_t_2;
- __pyx_t_2 = 0;
- __pyx_v_rtid = __pyx_t_8;
- __pyx_v_rstart = __pyx_t_9;
- __pyx_v_rend = __pyx_t_10;
} else {
- __pyx_t_11 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ Py_ssize_t index = -1;
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_2 = __Pyx_UnpackItem(__pyx_t_11, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_UnpackItem(__pyx_t_11, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = __Pyx_UnpackItem(__pyx_t_11, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __Pyx_UnpackItem(__pyx_t_11, 3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__Pyx_EndUnpack(__pyx_t_11, 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __Pyx_DECREF(__pyx_v_region);
- __pyx_v_region = __pyx_t_2;
- __pyx_t_2 = 0;
- __pyx_v_rtid = __pyx_t_10;
- __pyx_v_rstart = __pyx_t_9;
- __pyx_v_rend = __pyx_t_8;
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ goto __pyx_L5_unpacking_done;
+ __pyx_L4_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5_unpacking_done:;
+ }
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_v_has_coord = __pyx_t_10;
+ __pyx_v_rtid = __pyx_t_11;
+ __pyx_v_rstart = __pyx_t_12;
+ __pyx_v_rend = __pyx_t_13;
+
+ /* "csamtools.pyx":929
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ *
+ * if self.isstream: reopen = False # <<<<<<<<<<<<<<
+ * else: reopen = True
+ *
+ */
+ if (__pyx_v_self->isstream) {
+ __pyx_v_reopen = 0;
+ goto __pyx_L6;
}
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":849
+ /* "csamtools.pyx":930
*
- * cdef int counter
- * counter = 0; # <<<<<<<<<<<<<<
+ * if self.isstream: reopen = False
+ * else: reopen = True # <<<<<<<<<<<<<<
*
* if self.isbam:
*/
- __pyx_v_counter = 0;
+ __pyx_v_reopen = 1;
+ }
+ __pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":851
- * counter = 0;
+ /* "csamtools.pyx":932
+ * else: reopen = True
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ if (__pyx_v_self->isbam) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":852
+ /* "csamtools.pyx":933
*
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
* raise ValueError( "fetch called on bamfile without index" )
*
*/
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_12 = (!__pyx_t_4);
- if (__pyx_t_12) {
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
- __pyx_t_13 = __pyx_t_4;
+ __pyx_t_14 = (!__pyx_t_4);
+ if (__pyx_t_14) {
+ __pyx_t_4 = (!__pyx_v_self->isremote);
+ __pyx_t_15 = __pyx_t_4;
} else {
- __pyx_t_13 = __pyx_t_12;
+ __pyx_t_15 = __pyx_t_14;
}
- __pyx_t_12 = __pyx_t_13;
+ __pyx_t_14 = __pyx_t_15;
} else {
- __pyx_t_12 = __pyx_t_3;
+ __pyx_t_14 = __pyx_t_3;
}
- if (__pyx_t_12) {
+ if (__pyx_t_14) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":853
+ /* "csamtools.pyx":934
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
*
- * if not region:
+ * if callback:
*/
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_57), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_30));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_kp_s_30));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_30));
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
__pyx_L8:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":855
+ /* "csamtools.pyx":936
* raise ValueError( "fetch called on bamfile without index" )
*
- * if not region: # <<<<<<<<<<<<<<
- * raise ValueError( "counting functionality requires a region/reference" )
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * if callback: # <<<<<<<<<<<<<<
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
*/
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = (!__pyx_t_12);
- if (__pyx_t_3) {
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_14) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":856
+ /* "csamtools.pyx":937
*
- * if not region:
- * raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
- * bam_fetch(self.samfile.x.bam,
+ * if callback:
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * return bam_fetch(self.samfile.x.bam,
*/
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_40));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_40));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_40));
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = (!__pyx_v_has_coord);
+ if (__pyx_t_14) {
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_59), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L10;
+ }
+ __pyx_L10:;
+
+ /* "csamtools.pyx":938
+ * if callback:
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
+ * return bam_fetch(self.samfile.x.bam,
+ * self.index,
+ */
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
- }
- __pyx_L9:;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_3 = (!__pyx_t_14);
+ if (__pyx_t_3) {
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_61), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L11;
+ }
+ __pyx_L11:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":857
- * if not region:
- * raise ValueError( "counting functionality requires a region/reference" )
- * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
- * bam_fetch(self.samfile.x.bam,
- * self.index,
+ /* "csamtools.pyx":939
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * return bam_fetch(self.samfile.x.bam, # <<<<<<<<<<<<<<
+ * self.index,
+ * rtid,
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_12 = (!__pyx_t_3);
- if (__pyx_t_12) {
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+
+ /* "csamtools.pyx":945
+ * rend,
+ * <void*>callback,
+ * fetch_callback ) # <<<<<<<<<<<<<<
+ * else:
+ * if has_coord:
+ */
+ __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ __pyx_r = __pyx_t_5;
+ __pyx_t_5 = 0;
+ goto __pyx_L0;
+ goto __pyx_L9;
}
- __pyx_L10:;
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":864
- * rend,
- * <void*>&counter,
- * count_callback ) # <<<<<<<<<<<<<<
- * return counter
- * else:
+ /* "csamtools.pyx":947
+ * fetch_callback )
+ * else:
+ * if has_coord: # <<<<<<<<<<<<<<
+ * return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
+ * else:
*/
- bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback);
+ if (__pyx_v_has_coord) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":865
- * <void*>&counter,
- * count_callback )
- * return counter # <<<<<<<<<<<<<<
- * else:
- * raise ValueError ("count for a region is not available for sam files" )
+ /* "csamtools.pyx":948
+ * else:
+ * if has_coord:
+ * return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen ) # <<<<<<<<<<<<<<
+ * else:
+ * if until_eof:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = PyInt_FromLong(__pyx_v_counter); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L0;
- goto __pyx_L7;
- }
- /*else*/ {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_5 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_r = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L0;
+ goto __pyx_L12;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":867
- * return counter
- * else:
- * raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
- *
- * def pileup( self,
+ /* "csamtools.pyx":950
+ * return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
+ * else:
+ * if until_eof: # <<<<<<<<<<<<<<
+ * return IteratorRowAll( self, reopen=reopen )
+ * else:
*/
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_41));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_kp_s_41));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_41));
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L7:;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("csamtools.Samfile.count");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_region);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":869
- * raise ValueError ("count for a region is not available for sam files" )
- *
- * def pileup( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing). \n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed \n for each column within the :term:`region`. \n\n Note that :term:`SAM` formatted files do not allow random access. \n In these files, if a *region* or *reference* are given an exception is raised.\n \n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask.\n\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the \n first base of the first read *not* necessarily the first base of the region used in the query.\n\n The maximum number of reads considered for pileup is *8000*. This limit is set by\n :term:`csamtools`.\n\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_reference = 0;
- PyObject *__pyx_v_start = 0;
- PyObject *__pyx_v_end = 0;
- PyObject *__pyx_v_region = 0;
- PyObject *__pyx_v_callback = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- bam_plbuf_t *__pyx_v_buf;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
- int __pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
- PyObject *__pyx_t_12 = NULL;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup");
- __Pyx_TraceCall("pileup", __pyx_f[0], 869);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[5] = {0,0,0,0,0};
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":870
- *
- * def pileup( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
- */
- values[0] = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":871
- * def pileup( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None,
- */
- values[1] = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":872
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None,
- * callback = None,
- */
- values[2] = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":873
- * start = None,
- * end = None,
- * region = None, # <<<<<<<<<<<<<<
- * callback = None,
- * **kwargs ):
+ /* "csamtools.pyx":951
+ * else:
+ * if until_eof:
+ * return IteratorRowAll( self, reopen=reopen ) # <<<<<<<<<<<<<<
+ * else:
+ * # AH: check - reason why no reopen for AllRefs?
*/
- values[3] = ((PyObject *)Py_None);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L13;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":874
- * end = None,
- * region = None,
- * callback = None, # <<<<<<<<<<<<<<
- * **kwargs ):
- * '''
+ /* "csamtools.pyx":954
+ * else:
+ * # AH: check - reason why no reopen for AllRefs?
+ * return IteratorRowAllRefs(self ) # , reopen=reopen ) # <<<<<<<<<<<<<<
+ * else:
+ * if has_coord:
*/
- values[4] = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (value) { values[0] = value; kw_args--; }
- }
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
- if (value) { values[3] = value; kw_args--; }
- }
- case 4:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__callback);
- if (value) { values[4] = value; kw_args--; }
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_6;
+ __pyx_t_6 = 0;
+ goto __pyx_L0;
+ }
+ __pyx_L13:;
}
+ __pyx_L12:;
}
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_reference = values[0];
- __pyx_v_start = values[1];
- __pyx_v_end = values[2];
- __pyx_v_region = values[3];
- __pyx_v_callback = values[4];
- } else {
+ __pyx_L9:;
+ goto __pyx_L7;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":870
+ /* "csamtools.pyx":956
+ * return IteratorRowAllRefs(self ) # , reopen=reopen )
+ * else:
+ * if has_coord: # <<<<<<<<<<<<<<
+ * raise ValueError ("fetching by region is not available for sam files" )
*
- * def pileup( self,
- * reference = None, # <<<<<<<<<<<<<<
- * start = None,
- * end = None,
*/
- __pyx_v_reference = ((PyObject *)Py_None);
+ if (__pyx_v_has_coord) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":871
- * def pileup( self,
- * reference = None,
- * start = None, # <<<<<<<<<<<<<<
- * end = None,
- * region = None,
- */
- __pyx_v_start = ((PyObject *)Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":872
- * reference = None,
- * start = None,
- * end = None, # <<<<<<<<<<<<<<
- * region = None,
- * callback = None,
+ /* "csamtools.pyx":957
+ * else:
+ * if has_coord:
+ * raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
+ *
+ * if callback:
*/
- __pyx_v_end = ((PyObject *)Py_None);
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_63), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_Raise(__pyx_t_6, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L14;
+ }
+ __pyx_L14:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":873
- * start = None,
- * end = None,
- * region = None, # <<<<<<<<<<<<<<
- * callback = None,
- * **kwargs ):
+ /* "csamtools.pyx":959
+ * raise ValueError ("fetching by region is not available for sam files" )
+ *
+ * if callback: # <<<<<<<<<<<<<<
+ * raise NotImplementedError( "callback not implemented yet" )
+ *
*/
- __pyx_v_region = ((PyObject *)Py_None);
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":874
- * end = None,
- * region = None,
- * callback = None, # <<<<<<<<<<<<<<
- * **kwargs ):
- * '''
+ /* "csamtools.pyx":960
+ *
+ * if callback:
+ * raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
+ *
+ * if self.samfile.header == NULL:
*/
- __pyx_v_callback = ((PyObject *)Py_None);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 5: __pyx_v_callback = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: __pyx_v_region = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_end = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: __pyx_v_start = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_65), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_Raise(__pyx_t_6, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L15;
}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.Samfile.pileup");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
+ __pyx_L15:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":921
- * cdef bam_plbuf_t *buf
+ /* "csamtools.pyx":962
+ * raise NotImplementedError( "callback not implemented yet" )
*
- * if not self._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
+ * if self.samfile.header == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "fetch called for samfile without header")
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
+ __pyx_t_3 = (__pyx_v_self->samfile->header == NULL);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":922
+ /* "csamtools.pyx":963
*
- * if not self._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if self.samfile.header == NULL:
+ * raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
*
- * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ * # check if targets are defined
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_67), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_Raise(__pyx_t_6, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L16;
+ }
+ __pyx_L16:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":924
- * raise ValueError( "I/O operation on closed file" )
- *
- * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":967
+ * # check if targets are defined
+ * # give warning, sam_read1 segfaults
+ * if self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
+ * warnings.warn( "fetch called for samfile without header")
*
- * if self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
- __Pyx_GIVEREF(__pyx_v_reference);
- __Pyx_INCREF(__pyx_v_start);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_start);
- __Pyx_GIVEREF(__pyx_v_start);
- __Pyx_INCREF(__pyx_v_end);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_end);
- __Pyx_GIVEREF(__pyx_v_end);
- __Pyx_INCREF(__pyx_v_region);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_v_region);
- __Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyTuple_CheckExact(__pyx_t_5) && likely(PyTuple_GET_SIZE(__pyx_t_5) == 4)) {
- PyObject* tuple = __pyx_t_5;
- __pyx_t_2 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_2);
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_1 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_1);
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = PyTuple_GET_ITEM(tuple, 2); __Pyx_INCREF(__pyx_t_6);
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = PyTuple_GET_ITEM(tuple, 3); __Pyx_INCREF(__pyx_t_7);
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_v_has_coord = __pyx_t_8;
- __pyx_v_rtid = __pyx_t_9;
- __pyx_v_rstart = __pyx_t_10;
- __pyx_v_rend = __pyx_t_11;
- } else {
- __pyx_t_12 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_2 = __Pyx_UnpackItem(__pyx_t_12, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_1 = __Pyx_UnpackItem(__pyx_t_12, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = __Pyx_UnpackItem(__pyx_t_12, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __Pyx_UnpackItem(__pyx_t_12, 3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__Pyx_EndUnpack(__pyx_t_12, 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_v_has_coord = __pyx_t_11;
- __pyx_v_rtid = __pyx_t_10;
- __pyx_v_rstart = __pyx_t_9;
- __pyx_v_rend = __pyx_t_8;
- }
+ __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":926
- * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
- *
- * if self.isbam: # <<<<<<<<<<<<<<
- * if not self._hasIndex(): raise ValueError( "no index available for pileup" )
+ /* "csamtools.pyx":968
+ * # give warning, sam_read1 segfaults
+ * if self.samfile.header.n_targets == 0:
+ * warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<<
*
+ * return IteratorRowAll( self, reopen=reopen )
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__warnings); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__warn); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_68), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L17;
+ }
+ __pyx_L17:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":927
+ /* "csamtools.pyx":970
+ * warnings.warn( "fetch called for samfile without header")
*
- * if self.isbam:
- * if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
+ * return IteratorRowAll( self, reopen=reopen ) # <<<<<<<<<<<<<<
*
- * if callback:
+ * def mate( self,
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_42));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_kp_s_42));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_42));
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
- }
- __pyx_L8:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":929
- * if not self._hasIndex(): raise ValueError( "no index available for pileup" )
- *
- * if callback: # <<<<<<<<<<<<<<
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
- *
- */
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_3) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":930
- *
- * if callback:
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
- *
- * buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback )
- */
- __pyx_t_3 = (!__pyx_v_has_coord);
- if (__pyx_t_3) {
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_31));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_31));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_31));
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
- }
- __pyx_L10:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":932
- * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
- *
- * buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback ) # <<<<<<<<<<<<<<
- * bam_fetch(self.samfile.x.bam,
- * self.index, rtid, rstart, rend,
- */
- __pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":935
- * bam_fetch(self.samfile.x.bam,
- * self.index, rtid, rstart, rend,
- * buf, pileup_fetch_callback ) # <<<<<<<<<<<<<<
- *
- * # finalize pileup
- */
- bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":938
- *
- * # finalize pileup
- * bam_plbuf_push( NULL, buf) # <<<<<<<<<<<<<<
- * bam_plbuf_destroy(buf)
- * else:
- */
- bam_plbuf_push(NULL, __pyx_v_buf);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":939
- * # finalize pileup
- * bam_plbuf_push( NULL, buf)
- * bam_plbuf_destroy(buf) # <<<<<<<<<<<<<<
- * else:
- * if has_coord:
- */
- bam_plbuf_destroy(__pyx_v_buf);
- goto __pyx_L9;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":941
- * bam_plbuf_destroy(buf)
- * else:
- * if has_coord: # <<<<<<<<<<<<<<
- * return IteratorColumnRegion( self,
- * tid = rtid,
- */
- if (__pyx_v_has_coord) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":942
- * else:
- * if has_coord:
- * return IteratorColumnRegion( self, # <<<<<<<<<<<<<<
- * tid = rtid,
- * start = rstart,
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":943
- * if has_coord:
- * return IteratorColumnRegion( self,
- * tid = rtid, # <<<<<<<<<<<<<<
- * start = rstart,
- * end = rend,
- */
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":944
- * return IteratorColumnRegion( self,
- * tid = rtid,
- * start = rstart, # <<<<<<<<<<<<<<
- * end = rend,
- * **kwargs )
- */
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":945
- * tid = rtid,
- * start = rstart,
- * end = rend, # <<<<<<<<<<<<<<
- * **kwargs )
- * else:
- */
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":946
- * start = rstart,
- * end = rend,
- * **kwargs ) # <<<<<<<<<<<<<<
- * else:
- * return IteratorColumnAllRefs(self, **kwargs )
- */
- if (PyDict_Update(((PyObject *)__pyx_t_5), ((PyObject *)__pyx_v_kwargs)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnRegion)), __pyx_t_7, ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_r = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L0;
- goto __pyx_L11;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":948
- * **kwargs )
- * else:
- * return IteratorColumnAllRefs(self, **kwargs ) # <<<<<<<<<<<<<<
- *
- * else:
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_5 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), __pyx_t_6, ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_r = __pyx_t_5;
- __pyx_t_5 = 0;
- goto __pyx_L0;
- }
- __pyx_L11:;
- }
- __pyx_L9:;
- goto __pyx_L7;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":951
- *
- * else:
- * raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
- *
- * def close( self ):
- */
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_43));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
- __pyx_t_6 = PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L0;
}
__pyx_L7:;
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_12);
- __Pyx_AddTraceback("csamtools.Samfile.pileup");
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_AddTraceback("csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":953
- * raise NotImplementedError( "pileup of samfiles not implemented yet" )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_22mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("mate (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_22mate(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":972
+ * return IteratorRowAll( self, reopen=reopen )
*
- * def close( self ): # <<<<<<<<<<<<<<
- * '''
- * closes the :class:`pysam.Samfile`.'''
+ * def mate( self, # <<<<<<<<<<<<<<
+ * AlignedRead read ):
+ * '''return the mate of :class:`AlignedRead` *read*.
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read) {
+ uint32_t __pyx_v_flag;
+ __pyx_t_9csamtools_MateData __pyx_v_mate_data;
+ int __pyx_v_x;
+ struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close");
- __Pyx_TraceCall("close", __pyx_f[0], 953);
+ __Pyx_RefNannySetupContext("mate", 0);
+ __Pyx_TraceCall("mate", __pyx_f[0], 972);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":956
+ /* "csamtools.pyx":985
+ *
* '''
- * closes the :class:`pysam.Samfile`.'''
- * if self.samfile != NULL: # <<<<<<<<<<<<<<
- * samclose( self.samfile )
- * bam_index_destroy(self.index);
- */
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
- if (__pyx_t_1) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":957
- * closes the :class:`pysam.Samfile`.'''
- * if self.samfile != NULL:
- * samclose( self.samfile ) # <<<<<<<<<<<<<<
- * bam_index_destroy(self.index);
- * self.samfile = NULL
+ * cdef uint32_t flag = read._delegate.core.flag # <<<<<<<<<<<<<<
+ *
+ * if flag & BAM_FPAIRED == 0:
*/
- samclose(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile);
+ __pyx_v_flag = __pyx_v_read->_delegate->core.flag;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":958
- * if self.samfile != NULL:
- * samclose( self.samfile )
- * bam_index_destroy(self.index); # <<<<<<<<<<<<<<
- * self.samfile = NULL
+ /* "csamtools.pyx":987
+ * cdef uint32_t flag = read._delegate.core.flag
*
+ * if flag & BAM_FPAIRED == 0: # <<<<<<<<<<<<<<
+ * raise ValueError( "read %s: is unpaired" % (read.qname))
+ * if flag & BAM_FMUNMAP != 0:
*/
- bam_index_destroy(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index);
+ __pyx_t_1 = ((__pyx_v_flag & 1) == 0);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":959
- * samclose( self.samfile )
- * bam_index_destroy(self.index);
- * self.samfile = NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":988
*
- * def __dealloc__( self ):
+ * if flag & BAM_FPAIRED == 0:
+ * raise ValueError( "read %s: is unpaired" % (read.qname)) # <<<<<<<<<<<<<<
+ * if flag & BAM_FMUNMAP != 0:
+ * raise ValueError( "mate %s: is unmapped" % (read.qname))
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
- goto __pyx_L5;
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_L3:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":961
- * self.samfile = NULL
+ /* "csamtools.pyx":989
+ * if flag & BAM_FPAIRED == 0:
+ * raise ValueError( "read %s: is unpaired" % (read.qname))
+ * if flag & BAM_FMUNMAP != 0: # <<<<<<<<<<<<<<
+ * raise ValueError( "mate %s: is unmapped" % (read.qname))
*
- * def __dealloc__( self ): # <<<<<<<<<<<<<<
- * # remember: dealloc cannot call other methods
- * # note: no doc string
*/
+ __pyx_t_1 = ((__pyx_v_flag & 8) != 0);
+ if (__pyx_t_1) {
-static void __pyx_pf_9csamtools_7Samfile___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_7Samfile___dealloc__(PyObject *__pyx_v_self) {
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 961);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":965
- * # note: no doc string
- * # note: __del__ is not called.
- * self.close() # <<<<<<<<<<<<<<
- * bam_destroy1(self.b)
- * if self._filename != NULL: free( self._filename )
+ /* "csamtools.pyx":990
+ * raise ValueError( "read %s: is unpaired" % (read.qname))
+ * if flag & BAM_FMUNMAP != 0:
+ * raise ValueError( "mate %s: is unmapped" % (read.qname)) # <<<<<<<<<<<<<<
+ *
+ * cdef MateData mate_data
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 965; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 965; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":966
- * # note: __del__ is not called.
- * self.close()
- * bam_destroy1(self.b) # <<<<<<<<<<<<<<
- * if self._filename != NULL: free( self._filename )
+ /* "csamtools.pyx":994
+ * cdef MateData mate_data
*
+ * mate_data.name = <char *>bam1_qname(read._delegate) # <<<<<<<<<<<<<<
+ * mate_data.mate = NULL
+ * # xor flags to get the other mate
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
+ __pyx_v_mate_data.name = ((char *)bam1_qname(__pyx_v_read->_delegate));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":967
- * self.close()
- * bam_destroy1(self.b)
- * if self._filename != NULL: free( self._filename ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":995
*
- * cpdef int write( self, AlignedRead read ) except -1:
+ * mate_data.name = <char *>bam1_qname(read._delegate)
+ * mate_data.mate = NULL # <<<<<<<<<<<<<<
+ * # xor flags to get the other mate
+ * cdef int x = BAM_FREAD1 + BAM_FREAD2
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
- if (__pyx_t_3) {
- free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__dealloc__");
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
+ __pyx_v_mate_data.mate = NULL;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":969
- * if self._filename != NULL: free( self._filename )
+ /* "csamtools.pyx":997
+ * mate_data.mate = NULL
+ * # xor flags to get the other mate
+ * cdef int x = BAM_FREAD1 + BAM_FREAD2 # <<<<<<<<<<<<<<
+ * mate_data.flag = ( flag ^ x) & x
*
- * cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
- * '''
- * write a single :class:`pysam.AlignedRead` to disk.
*/
+ __pyx_v_x = 192;
-static PyObject *__pyx_pf_9csamtools_7Samfile_write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
- int __pyx_t_5;
- int __pyx_t_6;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write");
- __Pyx_TraceCall("write", __pyx_f[0], 969);
- /* Check if called by wrapper */
- if (unlikely(__pyx_skip_dispatch)) ;
- /* Check if overriden in Python */
- else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (void *)&__pyx_pf_9csamtools_7Samfile_write)) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_read));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_read));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_read));
- __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_r = __pyx_t_4;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L0;
- }
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- }
+ /* "csamtools.pyx":998
+ * # xor flags to get the other mate
+ * cdef int x = BAM_FREAD1 + BAM_FREAD2
+ * mate_data.flag = ( flag ^ x) & x # <<<<<<<<<<<<<<
+ *
+ * bam_fetch(self.samfile.x.bam,
+ */
+ __pyx_v_mate_data.flag = ((__pyx_v_flag ^ __pyx_v_x) & __pyx_v_x);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":975
- * returns the number of bytes written.
- * '''
- * if not self._isOpen(): # <<<<<<<<<<<<<<
- * return 0
+ /* "csamtools.pyx":1006
+ * read._delegate.core.mpos + 1,
+ * <void*>&mate_data,
+ * mate_callback ) # <<<<<<<<<<<<<<
*
+ * if mate_data.mate == NULL:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = (!__pyx_t_5);
- if (__pyx_t_6) {
+ bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":976
- * '''
- * if not self._isOpen():
- * return 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1008
+ * mate_callback )
+ *
+ * if mate_data.mate == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "mate not found" )
*
- * return samwrite( self.samfile, read._delegate )
*/
- __pyx_r = 0;
- goto __pyx_L0;
- goto __pyx_L3;
- }
- __pyx_L3:;
+ __pyx_t_1 = (__pyx_v_mate_data.mate == NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":978
- * return 0
+ /* "csamtools.pyx":1009
*
- * return samwrite( self.samfile, read._delegate ) # <<<<<<<<<<<<<<
+ * if mate_data.mate == NULL:
+ * raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
*
- * def __enter__(self):
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
- __pyx_r = samwrite(__pyx_v_self->samfile, __pyx_v_read->_delegate);
- goto __pyx_L0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_72), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_WriteUnraisable("csamtools.Samfile.write");
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":1011
+ * raise ValueError( "mate not found" )
+ *
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
+ * dest._delegate = mate_data.mate
+ * return dest
+ */
+ __pyx_t_2 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_2);
+ __pyx_t_2 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":969
- * if self._filename != NULL: free( self._filename )
+ /* "csamtools.pyx":1012
+ *
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
+ * dest._delegate = mate_data.mate # <<<<<<<<<<<<<<
+ * return dest
*
- * cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
- * '''
- * write a single :class:`pysam.AlignedRead` to disk.
*/
+ __pyx_v_dest->_delegate = __pyx_v_mate_data.mate;
-static PyObject *__pyx_pf_9csamtools_7Samfile_write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write");
- __Pyx_TraceCall("write", __pyx_f[0], 969);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /* "csamtools.pyx":1013
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
+ * dest._delegate = mate_data.mate
+ * return dest # <<<<<<<<<<<<<<
+ *
+ * def count( self,
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read), 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_v_dest));
+ __pyx_r = ((PyObject *)__pyx_v_dest);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Samfile.write");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.Samfile.mate", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF((PyObject *)__pyx_v_dest);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":980
- * return samwrite( self.samfile, read._delegate )
- *
- * def __enter__(self): # <<<<<<<<<<<<<<
- * return self
- *
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile___enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile___enter__[] = "Samfile.__enter__(self)";
-static PyObject *__pyx_pf_9csamtools_7Samfile___enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__enter__");
- __Pyx_TraceCall("__enter__", __pyx_f[0], 980);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_24count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_reference = 0;
+ PyObject *__pyx_v_start = 0;
+ PyObject *__pyx_v_end = 0;
+ PyObject *__pyx_v_region = 0;
+ PyObject *__pyx_v_until_eof = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("count (wrapper)", 0);
+ {
+ PyObject* values[5] = {0,0,0,0,0};
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":981
- *
- * def __enter__(self):
- * return self # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1016
*
- * def __exit__(self, exc_type, exc_value, traceback):
+ * def count( self,
+ * reference = None, # <<<<<<<<<<<<<<
+ * start = None,
+ * end = None,
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
- goto __pyx_L0;
+ values[0] = ((PyObject *)Py_None);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":1017
+ * def count( self,
+ * reference = None,
+ * start = None, # <<<<<<<<<<<<<<
+ * end = None,
+ * region = None,
+ */
+ values[1] = ((PyObject *)Py_None);
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":983
- * return self
- *
- * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
- * self.close()
- * return False
+ /* "csamtools.pyx":1018
+ * reference = None,
+ * start = None,
+ * end = None, # <<<<<<<<<<<<<<
+ * region = None,
+ * until_eof = False ):
*/
+ values[2] = ((PyObject *)Py_None);
-static PyObject *__pyx_pf_9csamtools_7Samfile___exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile___exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
-static PyObject *__pyx_pf_9csamtools_7Samfile___exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_exc_type = 0;
- PyObject *__pyx_v_exc_value = 0;
- PyObject *__pyx_v_traceback = 0;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__exit__");
- __Pyx_TraceCall("__exit__", __pyx_f[0], 983);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[3] = {0,0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_value);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__traceback);
- if (likely(values[2])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_exc_type = values[0];
- __pyx_v_exc_value = values[1];
- __pyx_v_traceback = values[2];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_exc_type = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_exc_value = PyTuple_GET_ITEM(__pyx_args, 1);
- __pyx_v_traceback = PyTuple_GET_ITEM(__pyx_args, 2);
+ /* "csamtools.pyx":1019
+ * start = None,
+ * end = None,
+ * region = None, # <<<<<<<<<<<<<<
+ * until_eof = False ):
+ * '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
+ */
+ values[3] = ((PyObject *)Py_None);
+ values[4] = __pyx_k_73;
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
+ if (value) { values[0] = value; kw_args--; }
+ }
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__until_eof);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_reference = values[0];
+ __pyx_v_start = values[1];
+ __pyx_v_end = values[2];
+ __pyx_v_region = values[3];
+ __pyx_v_until_eof = values[4];
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("count", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.__exit__");
+ __Pyx_AddTraceback("csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":984
- *
- * def __exit__(self, exc_type, exc_value, traceback):
- * self.close() # <<<<<<<<<<<<<<
- * return False
- *
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":985
- * def __exit__(self, exc_type, exc_value, traceback):
- * self.close()
- * return False # <<<<<<<<<<<<<<
- *
- * ###############################################################
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__exit__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_24count(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_until_eof);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":994
- * property filename:
- * '''number of :term:`filename` associated with this object.'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self._filename
+/* "csamtools.pyx":1015
+ * return dest
+ *
+ * def count( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof) {
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_counter;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 994);
+ __Pyx_RefNannySetupContext("count", 0);
+ __Pyx_TraceCall("count", __pyx_f[0], 1015);
+ __Pyx_INCREF(__pyx_v_region);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":995
- * '''number of :term:`filename` associated with this object.'''
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * return self._filename
+ /* "csamtools.pyx":1033
+ * cdef int rend
+ *
+ * if not self._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":1034
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ */
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_74), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":996
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self._filename # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1036
+ * raise ValueError( "I/O operation on closed file" )
*
- * property nreferences:
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.filename.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1000
- * property nreferences:
- * '''number of :term:`reference` sequences in the file.'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self.samfile.header.n_targets
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1000);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1001
- * '''number of :term:`reference` sequences in the file.'''
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * return self.samfile.header.n_targets
+ * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
+ * cdef int counter
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_reference);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
+ __Pyx_GIVEREF(__pyx_v_reference);
+ __Pyx_INCREF(__pyx_v_start);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_start);
+ __Pyx_GIVEREF(__pyx_v_start);
+ __Pyx_INCREF(__pyx_v_end);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_end);
+ __Pyx_GIVEREF(__pyx_v_end);
+ __Pyx_INCREF(__pyx_v_region);
+ PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
+ __Pyx_GIVEREF(__pyx_v_region);
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
+ PyObject* sequence = __pyx_t_5;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+ if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+ if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_6 = PyList_GET_ITEM(sequence, 2);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 3);
+ }
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ goto __pyx_L5_unpacking_done;
+ __pyx_L4_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5_unpacking_done:;
}
- __pyx_L5:;
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_v_region);
+ __pyx_v_region = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __pyx_v_rtid = __pyx_t_10;
+ __pyx_v_rstart = __pyx_t_11;
+ __pyx_v_rend = __pyx_t_12;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1002
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self.samfile.header.n_targets # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1039
*
- * property references:
+ * cdef int counter
+ * counter = 0; # <<<<<<<<<<<<<<
+ *
+ * if self.isbam:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.nreferences.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_v_counter = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1006
- * property references:
- * """tuple with the names of :term:`reference` sequences."""
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * t = []
+ /* "csamtools.pyx":1041
+ * counter = 0;
+ *
+ * if self.isbam: # <<<<<<<<<<<<<<
+ * if not until_eof and not self._hasIndex() and not self.isremote:
+ * raise ValueError( "fetch called on bamfile without index" )
*/
+ if (__pyx_v_self->isbam) {
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_v_t;
- long __pyx_v_x;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int32_t __pyx_t_5;
- int __pyx_t_6;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1006);
- __pyx_v_t = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1007
- * """tuple with the names of :term:`reference` sequences."""
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * t = []
- * for x from 0 <= x < self.samfile.header.n_targets:
+ /* "csamtools.pyx":1042
+ *
+ * if self.isbam:
+ * if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
+ * raise ValueError( "fetch called on bamfile without index" )
+ *
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1008
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * t = [] # <<<<<<<<<<<<<<
- * for x from 0 <= x < self.samfile.header.n_targets:
- * t.append( self.samfile.header.target_name[x] )
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_13 = (!__pyx_t_4);
+ if (__pyx_t_13) {
+ __pyx_t_4 = (!__pyx_v_self->isremote);
+ __pyx_t_14 = __pyx_t_4;
+ } else {
+ __pyx_t_14 = __pyx_t_13;
+ }
+ __pyx_t_13 = __pyx_t_14;
+ } else {
+ __pyx_t_13 = __pyx_t_3;
+ }
+ if (__pyx_t_13) {
+
+ /* "csamtools.pyx":1043
+ * if self.isbam:
+ * if not until_eof and not self._hasIndex() and not self.isremote:
+ * raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
+ *
+ * if not region:
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_t));
- __pyx_v_t = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_75), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1009
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * t = []
- * for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
- * t.append( self.samfile.header.target_name[x] )
- * return tuple(t)
+ /* "csamtools.pyx":1045
+ * raise ValueError( "fetch called on bamfile without index" )
+ *
+ * if not region: # <<<<<<<<<<<<<<
+ * raise ValueError( "counting functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
*/
- __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
- for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (!__pyx_t_13);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1010
- * t = []
- * for x from 0 <= x < self.samfile.header.n_targets:
- * t.append( self.samfile.header.target_name[x] ) # <<<<<<<<<<<<<<
- * return tuple(t)
+ /* "csamtools.pyx":1046
*
+ * if not region:
+ * raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * bam_fetch(self.samfile.x.bam,
*/
- if (unlikely(__pyx_v_t == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1010; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L8;
}
- __pyx_t_1 = PyBytes_FromString((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1010; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_6 = PyList_Append(((PyObject *)__pyx_v_t), ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1010; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_L8:;
+
+ /* "csamtools.pyx":1047
+ * if not region:
+ * raise ValueError( "counting functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
+ * bam_fetch(self.samfile.x.bam,
+ * self.index,
+ */
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_13 = (!__pyx_t_3);
+ if (__pyx_t_13) {
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_78), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
+
+ /* "csamtools.pyx":1054
+ * rend,
+ * <void*>&counter,
+ * count_callback ) # <<<<<<<<<<<<<<
+ * return counter
+ * else:
+ */
+ bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback);
+
+ /* "csamtools.pyx":1055
+ * <void*>&counter,
+ * count_callback )
+ * return counter # <<<<<<<<<<<<<<
+ * else:
+ * raise ValueError ("count for a region is not available for sam files" )
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_counter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_r = __pyx_t_5;
+ __pyx_t_5 = 0;
+ goto __pyx_L0;
+ goto __pyx_L6;
}
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1011
- * for x from 0 <= x < self.samfile.header.n_targets:
- * t.append( self.samfile.header.target_name[x] )
- * return tuple(t) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1057
+ * return counter
+ * else:
+ * raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
*
- * property lengths:
+ * def pileup( self,
*/
- __Pyx_XDECREF(__pyx_r);
- if (unlikely(__pyx_v_t == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_80), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __pyx_L6:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.references.__get__");
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_AddTraceback("csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_t);
+ __Pyx_XDECREF(__pyx_v_region);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1017
- * :attr:`pysam.Samfile.references`
- * """
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * t = []
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_26pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed\n for each column within the :term:`region`.\n\n Note that :term:`SAM` formatted files do not allow random access.\n In these files, if a *region* or *reference* are given an exception is raised.\n\n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances.\n Possible options for the stepper are\n\n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask if mask=True.\n\n max_depth\n Maximum read depth permitted. The default limit is *8000*.\n\n truncate\n By default, the samtools pileup engine outputs all reads overlapping a region (see note below).\n If truncate is True and a region is given, only output columns in the exact region\n specificied.\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the\n first base of the first read *not* necessarily the first base of the region used in the query.\n\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_reference = 0;
+ PyObject *__pyx_v_start = 0;
+ PyObject *__pyx_v_end = 0;
+ PyObject *__pyx_v_region = 0;
+ PyObject *__pyx_v_callback = 0;
+ PyObject *__pyx_v_kwargs = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("pileup (wrapper)", 0);
+ __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ {
+ PyObject* values[5] = {0,0,0,0,0};
+
+ /* "csamtools.pyx":1060
+ *
+ * def pileup( self,
+ * reference = None, # <<<<<<<<<<<<<<
+ * start = None,
+ * end = None,
*/
+ values[0] = ((PyObject *)Py_None);
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_v_t;
- long __pyx_v_x;
+ /* "csamtools.pyx":1061
+ * def pileup( self,
+ * reference = None,
+ * start = None, # <<<<<<<<<<<<<<
+ * end = None,
+ * region = None,
+ */
+ values[1] = ((PyObject *)Py_None);
+
+ /* "csamtools.pyx":1062
+ * reference = None,
+ * start = None,
+ * end = None, # <<<<<<<<<<<<<<
+ * region = None,
+ * callback = None,
+ */
+ values[2] = ((PyObject *)Py_None);
+
+ /* "csamtools.pyx":1063
+ * start = None,
+ * end = None,
+ * region = None, # <<<<<<<<<<<<<<
+ * callback = None,
+ * **kwargs ):
+ */
+ values[3] = ((PyObject *)Py_None);
+
+ /* "csamtools.pyx":1064
+ * end = None,
+ * region = None,
+ * callback = None, # <<<<<<<<<<<<<<
+ * **kwargs ):
+ * '''
+ */
+ values[4] = ((PyObject *)Py_None);
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
+ if (value) { values[0] = value; kw_args--; }
+ }
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__region);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__callback);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_reference = values[0];
+ __pyx_v_start = values[1];
+ __pyx_v_end = values[2];
+ __pyx_v_region = values[3];
+ __pyx_v_callback = values[4];
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
+ __Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_26pileup(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1059
+ * raise ValueError ("count for a region is not available for sam files" )
+ *
+ * def pileup( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs) {
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ bam_plbuf_t *__pyx_v_buf;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
- int32_t __pyx_t_5;
- int __pyx_t_6;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1017);
- __pyx_v_t = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("pileup", 0);
+ __Pyx_TraceCall("pileup", __pyx_f[0], 1059);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1018
- * """
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * t = []
- * for x from 0 <= x < self.samfile.header.n_targets:
+ /* "csamtools.pyx":1115
+ * cdef bam_plbuf_t *buf
+ *
+ * if not self._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
+ *
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":1116
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ */
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_81), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1019
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * t = [] # <<<<<<<<<<<<<<
- * for x from 0 <= x < self.samfile.header.n_targets:
- * t.append( self.samfile.header.target_len[x] )
+ /* "csamtools.pyx":1118
+ * raise ValueError( "I/O operation on closed file" )
+ *
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
+ *
+ * if self.isbam:
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_t));
- __pyx_v_t = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1020
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * t = []
- * for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
- * t.append( self.samfile.header.target_len[x] )
- * return tuple(t)
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_reference);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
+ __Pyx_GIVEREF(__pyx_v_reference);
+ __Pyx_INCREF(__pyx_v_start);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_start);
+ __Pyx_GIVEREF(__pyx_v_start);
+ __Pyx_INCREF(__pyx_v_end);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_end);
+ __Pyx_GIVEREF(__pyx_v_end);
+ __Pyx_INCREF(__pyx_v_region);
+ PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
+ __Pyx_GIVEREF(__pyx_v_region);
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
+ PyObject* sequence = __pyx_t_5;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+ if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+ if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_6 = PyList_GET_ITEM(sequence, 2);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 3);
+ }
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ goto __pyx_L5_unpacking_done;
+ __pyx_L4_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5_unpacking_done:;
+ }
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_v_has_coord = __pyx_t_10;
+ __pyx_v_rtid = __pyx_t_11;
+ __pyx_v_rstart = __pyx_t_12;
+ __pyx_v_rend = __pyx_t_13;
+
+ /* "csamtools.pyx":1120
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ *
+ * if self.isbam: # <<<<<<<<<<<<<<
+ * if not self._hasIndex(): raise ValueError( "no index available for pileup" )
+ *
*/
- __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
- for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
+ if (__pyx_v_self->isbam) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1021
- * t = []
- * for x from 0 <= x < self.samfile.header.n_targets:
- * t.append( self.samfile.header.target_len[x] ) # <<<<<<<<<<<<<<
- * return tuple(t)
+ /* "csamtools.pyx":1121
+ *
+ * if self.isbam:
+ * if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
*
+ * if callback:
*/
- if (unlikely(__pyx_v_t == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_83), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L7;
}
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyList_Append(((PyObject *)__pyx_v_t), __pyx_t_1); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_L7:;
+
+ /* "csamtools.pyx":1123
+ * if not self._hasIndex(): raise ValueError( "no index available for pileup" )
+ *
+ * if callback: # <<<<<<<<<<<<<<
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
+ *
+ */
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
+
+ /* "csamtools.pyx":1124
+ *
+ * if callback:
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
+ *
+ * buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback )
+ */
+ __pyx_t_3 = (!__pyx_v_has_coord);
+ if (__pyx_t_3) {
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_84), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
+
+ /* "csamtools.pyx":1126
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
+ *
+ * buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback ) # <<<<<<<<<<<<<<
+ * bam_fetch(self.samfile.x.bam,
+ * self.index, rtid, rstart, rend,
+ */
+ __pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
+
+ /* "csamtools.pyx":1129
+ * bam_fetch(self.samfile.x.bam,
+ * self.index, rtid, rstart, rend,
+ * buf, pileup_fetch_callback ) # <<<<<<<<<<<<<<
+ *
+ * # finalize pileup
+ */
+ bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback);
+
+ /* "csamtools.pyx":1132
+ *
+ * # finalize pileup
+ * bam_plbuf_push( NULL, buf) # <<<<<<<<<<<<<<
+ * bam_plbuf_destroy(buf)
+ * else:
+ */
+ bam_plbuf_push(NULL, __pyx_v_buf);
+
+ /* "csamtools.pyx":1133
+ * # finalize pileup
+ * bam_plbuf_push( NULL, buf)
+ * bam_plbuf_destroy(buf) # <<<<<<<<<<<<<<
+ * else:
+ * if has_coord:
+ */
+ bam_plbuf_destroy(__pyx_v_buf);
+ goto __pyx_L8;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":1135
+ * bam_plbuf_destroy(buf)
+ * else:
+ * if has_coord: # <<<<<<<<<<<<<<
+ * return IteratorColumnRegion( self,
+ * tid = rtid,
+ */
+ if (__pyx_v_has_coord) {
+
+ /* "csamtools.pyx":1136
+ * else:
+ * if has_coord:
+ * return IteratorColumnRegion( self, # <<<<<<<<<<<<<<
+ * tid = rtid,
+ * start = rstart,
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+
+ /* "csamtools.pyx":1140
+ * start = rstart,
+ * end = rend,
+ * **kwargs ) # <<<<<<<<<<<<<<
+ * else:
+ * return IteratorColumnAllRefs(self, **kwargs )
+ */
+ __pyx_t_5 = PyDict_Copy(((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+
+ /* "csamtools.pyx":1137
+ * if has_coord:
+ * return IteratorColumnRegion( self,
+ * tid = rtid, # <<<<<<<<<<<<<<
+ * start = rstart,
+ * end = rend,
+ */
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid)))) {
+ __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__tid)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+
+ /* "csamtools.pyx":1138
+ * return IteratorColumnRegion( self,
+ * tid = rtid,
+ * start = rstart, # <<<<<<<<<<<<<<
+ * end = rend,
+ * **kwargs )
+ */
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start)))) {
+ __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__start)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+
+ /* "csamtools.pyx":1139
+ * tid = rtid,
+ * start = rstart,
+ * end = rend, # <<<<<<<<<<<<<<
+ * **kwargs )
+ * else:
+ */
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end)))) {
+ __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__end)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_r = __pyx_t_6;
+ __pyx_t_6 = 0;
+ goto __pyx_L0;
+ goto __pyx_L10;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":1142
+ * **kwargs )
+ * else:
+ * return IteratorColumnAllRefs(self, **kwargs ) # <<<<<<<<<<<<<<
+ *
+ * else:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_5 = ((PyObject *)__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_r = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L0;
+ }
+ __pyx_L10:;
+ }
+ __pyx_L8:;
+ goto __pyx_L6;
}
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1022
- * for x from 0 <= x < self.samfile.header.n_targets:
- * t.append( self.samfile.header.target_len[x] )
- * return tuple(t) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1145
*
- * property text:
+ * else:
+ * raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
+ *
+ * def close( self ):
*/
- __Pyx_XDECREF(__pyx_r);
- if (unlikely(__pyx_v_t == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __pyx_L6:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.lengths.__get__");
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_t);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1026
- * property text:
- * '''full contents of the :term:`sam file` header as a string.'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return PyString_FromStringAndSize(self.samfile.header.text, self.samfile.header.l_text)
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_28close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
+static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("close (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_28close(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1147
+ * raise NotImplementedError( "pileup of samfiles not implemented yet" )
+ *
+ * def close( self ): # <<<<<<<<<<<<<<
+ * '''
+ * closes the :class:`pysam.Samfile`.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1026);
+ __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_TraceCall("close", __pyx_f[0], 1147);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1027
- * '''full contents of the :term:`sam file` header as a string.'''
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * return PyString_FromStringAndSize(self.samfile.header.text, self.samfile.header.l_text)
- *
+ /* "csamtools.pyx":1150
+ * '''
+ * closes the :class:`pysam.Samfile`.'''
+ * if self.samfile != NULL: # <<<<<<<<<<<<<<
+ * samclose( self.samfile )
+ * bam_index_destroy(self.index);
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1027; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1027; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1027; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1027; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1027; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1027; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_1 = (__pyx_v_self->samfile != NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1028
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return PyString_FromStringAndSize(self.samfile.header.text, self.samfile.header.l_text) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1151
+ * closes the :class:`pysam.Samfile`.'''
+ * if self.samfile != NULL:
+ * samclose( self.samfile ) # <<<<<<<<<<<<<<
+ * bam_index_destroy(self.index);
+ * self.samfile = NULL
+ */
+ samclose(__pyx_v_self->samfile);
+
+ /* "csamtools.pyx":1152
+ * if self.samfile != NULL:
+ * samclose( self.samfile )
+ * bam_index_destroy(self.index); # <<<<<<<<<<<<<<
+ * self.samfile = NULL
*
- * property header:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyString_FromStringAndSize(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->l_text); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ bam_index_destroy(__pyx_v_self->index);
+
+ /* "csamtools.pyx":1153
+ * samclose( self.samfile )
+ * bam_index_destroy(self.index);
+ * self.samfile = NULL # <<<<<<<<<<<<<<
+ *
+ * def __dealloc__( self ):
+ */
+ __pyx_v_self->samfile = NULL;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.text.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1034
- * a two-level dictionary.
- * '''
- * def __get__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+/* Python wrapper */
+static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_7Samfile_30__dealloc__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "csamtools.pyx":1155
+ * self.samfile = NULL
*
+ * def __dealloc__( self ): # <<<<<<<<<<<<<<
+ * # remember: dealloc cannot call other methods
+ * # note: no doc string
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_v_result;
- PyObject *__pyx_v_t;
- PyObject *__pyx_v_line;
- PyObject *__pyx_v_fields;
- PyObject *__pyx_v_record;
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_field;
- PyObject *__pyx_v_key;
- PyObject *__pyx_v_value;
- PyObject *__pyx_r = NULL;
+static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- Py_ssize_t __pyx_t_9;
- PyObject *__pyx_t_10 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1034);
- __pyx_v_result = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_t = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_line = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_fields = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_record = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_x = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_field = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_key = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_value = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1035
- * '''
- * def __get__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- *
- * result = {}
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1155);
+
+ /* "csamtools.pyx":1159
+ * # note: no doc string
+ * # note: __del__ is not called.
+ * self.close() # <<<<<<<<<<<<<<
+ * bam_destroy1(self.b)
+ * if self._filename != NULL: free( self._filename )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1037
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- *
- * result = {} # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1160
+ * # note: __del__ is not called.
+ * self.close()
+ * bam_destroy1(self.b) # <<<<<<<<<<<<<<
+ * if self._filename != NULL: free( self._filename )
*
- * if self.samfile.header.text != NULL:
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_result));
- __pyx_v_result = __pyx_t_1;
- __pyx_t_1 = 0;
+ bam_destroy1(__pyx_v_self->b);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1039
- * result = {}
+ /* "csamtools.pyx":1161
+ * self.close()
+ * bam_destroy1(self.b)
+ * if self._filename != NULL: free( self._filename ) # <<<<<<<<<<<<<<
*
- * if self.samfile.header.text != NULL: # <<<<<<<<<<<<<<
- * # convert to python string (note: call self.text to create 0-terminated string)
- * t = self.text
+ * cpdef int write( self, AlignedRead read ) except -1:
*/
- __pyx_t_4 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text != NULL);
- if (__pyx_t_4) {
+ __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ if (__pyx_t_3) {
+ free(__pyx_v_self->_filename);
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1041
- * if self.samfile.header.text != NULL:
- * # convert to python string (note: call self.text to create 0-terminated string)
- * t = self.text # <<<<<<<<<<<<<<
- * for line in t.split("\n"):
- * if not line.strip(): continue
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__text); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_1;
- __pyx_t_1 = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1042
- * # convert to python string (note: call self.text to create 0-terminated string)
- * t = self.text
- * for line in t.split("\n"): # <<<<<<<<<<<<<<
- * if not line.strip(): continue
- * assert line.startswith("@"), "header line without '@': '%s'" % line
+/* "csamtools.pyx":1163
+ * if self._filename != NULL: free( self._filename )
+ *
+ * cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
+ * '''
+ * write a single :class:`pysam.AlignedRead` to disk.
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_t, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ int __pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_TraceCall("write", __pyx_f[0], 1163);
+ /* Check if called by wrapper */
+ if (unlikely(__pyx_skip_dispatch)) ;
+ /* Check if overriden in Python */
+ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
- __pyx_t_6 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyList_CheckExact(__pyx_t_6) || PyTuple_CheckExact(__pyx_t_6)) {
- __pyx_t_5 = 0; __pyx_t_2 = __pyx_t_6; __Pyx_INCREF(__pyx_t_2);
- } else {
- __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write)) {
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- }
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_2))) {
- if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_6); __pyx_t_5++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_2))) {
- if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_6); __pyx_t_5++;
- } else {
- __pyx_t_6 = PyIter_Next(__pyx_t_2);
- if (!__pyx_t_6) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_6);
- }
- __Pyx_DECREF(__pyx_v_line);
- __pyx_v_line = __pyx_t_6;
- __pyx_t_6 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1043
- * t = self.text
- * for line in t.split("\n"):
- * if not line.strip(): continue # <<<<<<<<<<<<<<
- * assert line.startswith("@"), "header line without '@': '%s'" % line
- * fields = line[1:].split("\t")
- */
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
- goto __pyx_L7_continue;
- goto __pyx_L9;
- }
- __pyx_L9:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1044
- * for line in t.split("\n"):
- * if not line.strip(): continue
- * assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
- * fields = line[1:].split("\t")
- * record = fields[0]
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_44));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_kp_s_44));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_44));
- __pyx_t_7 = PyObject_Call(__pyx_t_1, __pyx_t_6, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(((PyObject *)__pyx_v_read));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_read));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_read));
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_r = __pyx_t_4;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (unlikely(!__pyx_t_3)) {
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_line); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ goto __pyx_L0;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1045
- * if not line.strip(): continue
- * assert line.startswith("@"), "header line without '@': '%s'" % line
- * fields = line[1:].split("\t") # <<<<<<<<<<<<<<
- * record = fields[0]
- * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
+ /* "csamtools.pyx":1169
+ * returns the number of bytes written.
+ * '''
+ * if not self._isOpen(): # <<<<<<<<<<<<<<
+ * return 0
+ *
*/
- __pyx_t_7 = PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_1));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_kp_s_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_1));
- __pyx_t_1 = PyObject_Call(__pyx_t_6, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_v_fields);
- __pyx_v_fields = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = (!__pyx_t_5);
+ if (__pyx_t_6) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1046
- * assert line.startswith("@"), "header line without '@': '%s'" % line
- * fields = line[1:].split("\t")
- * record = fields[0] # <<<<<<<<<<<<<<
- * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
+ /* "csamtools.pyx":1170
+ * '''
+ * if not self._isOpen():
+ * return 0 # <<<<<<<<<<<<<<
*
+ * return samwrite( self.samfile, read._delegate )
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_fields, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_v_record);
- __pyx_v_record = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1047
- * fields = line[1:].split("\t")
- * record = fields[0]
- * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1172
+ * return 0
*
- * # treat comments
+ * return samwrite( self.samfile, read._delegate ) # <<<<<<<<<<<<<<
+ *
+ * def __enter__(self):
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (unlikely(!__pyx_t_3)) {
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_record);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_record);
- __Pyx_GIVEREF(__pyx_v_record);
- __Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_line);
- __Pyx_GIVEREF(__pyx_v_line);
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_46), __pyx_t_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __pyx_r = samwrite(__pyx_v_self->samfile, __pyx_v_read->_delegate);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1050
- *
- * # treat comments
- * if record == "CO": # <<<<<<<<<<<<<<
- * if record not in result: result[record] = []
- * result[record].append( "\t".join( fields[1:] ) )
- */
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_3) {
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_WriteUnraisable("csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1051
- * # treat comments
- * if record == "CO":
- * if record not in result: result[record] = [] # <<<<<<<<<<<<<<
- * result[record].append( "\t".join( fields[1:] ) )
- * continue
- */
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- } else {
- __pyx_t_3 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- if (__pyx_t_3) {
- __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L11;
- }
- __pyx_L11:;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_32write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
+static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("write (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_32write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1052
- * if record == "CO":
- * if record not in result: result[record] = []
- * result[record].append( "\t".join( fields[1:] ) ) # <<<<<<<<<<<<<<
- * continue
+/* "csamtools.pyx":1163
+ * if self._filename != NULL: free( self._filename )
*
+ * cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
+ * '''
+ * write a single :class:`pysam.AlignedRead` to disk.
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_1, __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PyObject_Append(__pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1053
- * if record not in result: result[record] = []
- * result[record].append( "\t".join( fields[1:] ) )
- * continue # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_TraceCall("write", __pyx_f[0], 1163);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->write(__pyx_v_self, __pyx_v_read, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_34__enter__[] = "Samfile.__enter__(self)";
+static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__enter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_34__enter__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1174
+ * return samwrite( self.samfile, read._delegate )
+ *
+ * def __enter__(self): # <<<<<<<<<<<<<<
+ * return self
*
- * # the following is clumsy as generators do not work?
*/
- goto __pyx_L7_continue;
- goto __pyx_L10;
- }
- __pyx_L10:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1056
+static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__enter__", 0);
+ __Pyx_TraceCall("__enter__", __pyx_f[0], 1174);
+
+ /* "csamtools.pyx":1175
*
- * # the following is clumsy as generators do not work?
- * x = {} # <<<<<<<<<<<<<<
- * for field in fields[1:]:
- * key, value = field.split(":",1)
+ * def __enter__(self):
+ * return self # <<<<<<<<<<<<<<
+ *
+ * def __exit__(self, exc_type, exc_value, traceback):
*/
- __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1056; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __Pyx_DECREF(((PyObject *)__pyx_v_x));
- __pyx_v_x = __pyx_t_8;
- __pyx_t_8 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1057
- * # the following is clumsy as generators do not work?
- * x = {}
- * for field in fields[1:]: # <<<<<<<<<<<<<<
- * key, value = field.split(":",1)
- * # uppercase keys must be valid
- */
- __pyx_t_8 = PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
- __pyx_t_9 = 0; __pyx_t_6 = __pyx_t_8; __Pyx_INCREF(__pyx_t_6);
- } else {
- __pyx_t_9 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_36__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
+static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ CYTHON_UNUSED PyObject *__pyx_v_exc_type = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_exc_value = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_traceback = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__exit__ (wrapper)", 0);
+ {
+ PyObject* values[3] = {0,0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_6))) {
- if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_8); __pyx_t_9++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_6))) {
- if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_8); __pyx_t_9++;
- } else {
- __pyx_t_8 = PyIter_Next(__pyx_t_6);
- if (!__pyx_t_8) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_8);
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_value);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
- __Pyx_DECREF(__pyx_v_field);
- __pyx_v_field = __pyx_t_8;
- __pyx_t_8 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1058
- * x = {}
- * for field in fields[1:]:
- * key, value = field.split(":",1) # <<<<<<<<<<<<<<
- * # uppercase keys must be valid
- * # lowercase are permitted for user fields
- */
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_field, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_47));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_kp_s_47));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_47));
- __Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_int_1);
- __Pyx_GIVEREF(__pyx_int_1);
- __pyx_t_1 = PyObject_Call(__pyx_t_8, __pyx_t_7, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (PyTuple_CheckExact(__pyx_t_1) && likely(PyTuple_GET_SIZE(__pyx_t_1) == 2)) {
- PyObject* tuple = __pyx_t_1;
- __pyx_t_7 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_key);
- __pyx_v_key = __pyx_t_7;
- __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_8;
- __pyx_t_8 = 0;
- } else {
- __pyx_t_10 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_7 = __Pyx_UnpackItem(__pyx_t_10, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_UnpackItem(__pyx_t_10, 1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- if (__Pyx_EndUnpack(__pyx_t_10, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_v_key);
- __pyx_v_key = __pyx_t_7;
- __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_8;
- __pyx_t_8 = 0;
+ case 2:
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__traceback);
+ if (likely(values[2])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ }
+ __pyx_v_exc_type = values[0];
+ __pyx_v_exc_value = values[1];
+ __pyx_v_traceback = values[2];
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_36__exit__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_exc_type, __pyx_v_exc_value, __pyx_v_traceback);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1061
- * # uppercase keys must be valid
- * # lowercase are permitted for user fields
- * if key in VALID_HEADER_FIELDS[record]: # <<<<<<<<<<<<<<
- * x[key] = VALID_HEADER_FIELDS[record][key](value)
- * elif not key.isupper():
+/* "csamtools.pyx":1177
+ * return self
+ *
+ * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
+ * self.close()
+ * return False
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = ((PySequence_Contains(__pyx_t_8, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1062
- * # lowercase are permitted for user fields
- * if key in VALID_HEADER_FIELDS[record]:
- * x[key] = VALID_HEADER_FIELDS[record][key](value) # <<<<<<<<<<<<<<
- * elif not key.isupper():
- * x[key] = value
- */
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_1 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
- __Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_7 = PyObject_Call(__pyx_t_8, __pyx_t_1, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- goto __pyx_L14;
- }
+static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__exit__", 0);
+ __Pyx_TraceCall("__exit__", __pyx_f[0], 1177);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1063
- * if key in VALID_HEADER_FIELDS[record]:
- * x[key] = VALID_HEADER_FIELDS[record][key](value)
- * elif not key.isupper(): # <<<<<<<<<<<<<<
- * x[key] = value
- * else:
+ /* "csamtools.pyx":1178
+ *
+ * def __exit__(self, exc_type, exc_value, traceback):
+ * self.close() # <<<<<<<<<<<<<<
+ * return False
+ *
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1064
- * x[key] = VALID_HEADER_FIELDS[record][key](value)
- * elif not key.isupper():
- * x[key] = value # <<<<<<<<<<<<<<
- * else:
- * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
- */
- if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1066
- * x[key] = value
- * else:
- * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) ) # <<<<<<<<<<<<<<
- *
- * if VALID_HEADER_TYPES[record] == dict:
- */
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_key);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_key);
- __Pyx_GIVEREF(__pyx_v_key);
- __Pyx_INCREF(__pyx_v_record);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
- __Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_48), __pyx_t_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L14:;
- }
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1068
- * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
- *
- * if VALID_HEADER_TYPES[record] == dict: # <<<<<<<<<<<<<<
- * if record in result:
- * raise ValueError( "multiple '%s' lines are not permitted" % record )
- */
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetItem(__pyx_t_6, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)((PyObject*)&PyDict_Type)), Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1069
+ /* "csamtools.pyx":1179
+ * def __exit__(self, exc_type, exc_value, traceback):
+ * self.close()
+ * return False # <<<<<<<<<<<<<<
*
- * if VALID_HEADER_TYPES[record] == dict:
- * if record in result: # <<<<<<<<<<<<<<
- * raise ValueError( "multiple '%s' lines are not permitted" % record )
- * result[record] = x
+ * ###############################################################
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1069; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- } else {
- __pyx_t_4 = ((PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1069; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- if (__pyx_t_4) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1070
- * if VALID_HEADER_TYPES[record] == dict:
- * if record in result:
- * raise ValueError( "multiple '%s' lines are not permitted" % record ) # <<<<<<<<<<<<<<
- * result[record] = x
- * elif VALID_HEADER_TYPES[record] == list:
- */
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_49), __pyx_v_record); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
- }
- __pyx_L16:;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1071
- * if record in result:
- * raise ValueError( "multiple '%s' lines are not permitted" % record )
- * result[record] = x # <<<<<<<<<<<<<<
- * elif VALID_HEADER_TYPES[record] == list:
- * if record not in result: result[record] = []
- */
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
- }
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_8filename___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1072
- * raise ValueError( "multiple '%s' lines are not permitted" % record )
- * result[record] = x
- * elif VALID_HEADER_TYPES[record] == list: # <<<<<<<<<<<<<<
- * if record not in result: result[record] = []
- * result[record].append( x )
+/* "csamtools.pyx":1188
+ * property filename:
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return self._filename
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1072; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetItem(__pyx_t_6, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1072; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)((PyObject*)&PyList_Type)), Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1072; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1072; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1073
- * result[record] = x
- * elif VALID_HEADER_TYPES[record] == list:
- * if record not in result: result[record] = [] # <<<<<<<<<<<<<<
- * result[record].append( x )
- *
- */
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- } else {
- __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- if (__pyx_t_4) {
- __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_6)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- goto __pyx_L17;
- }
- __pyx_L17:;
+static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1188);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1074
- * elif VALID_HEADER_TYPES[record] == list:
- * if record not in result: result[record] = []
- * result[record].append( x ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1189
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self._filename
*
- * return result
*/
- __pyx_t_6 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1074; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = __Pyx_PyObject_Append(__pyx_t_6, ((PyObject *)__pyx_v_x)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1074; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- goto __pyx_L15;
- }
- __pyx_L15:;
- __pyx_L7_continue:;
- }
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_87), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1076
- * result[record].append( x )
- *
- * return result # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1190
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return self._filename # <<<<<<<<<<<<<<
*
- * def _buildLine( self, fields, record ):
+ * property nreferences:
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_result));
- __pyx_r = ((PyObject *)__pyx_v_result);
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.Samfile.header.__get__");
+ __Pyx_AddTraceback("csamtools.Samfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_result);
- __Pyx_DECREF(__pyx_v_t);
- __Pyx_DECREF(__pyx_v_line);
- __Pyx_DECREF(__pyx_v_fields);
- __Pyx_DECREF(__pyx_v_record);
- __Pyx_DECREF(__pyx_v_x);
- __Pyx_DECREF(__pyx_v_field);
- __Pyx_DECREF(__pyx_v_key);
- __Pyx_DECREF(__pyx_v_value);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1078
- * return result
- *
- * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
- * '''build a header line from *fields* dictionary for *record*'''
- *
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_11nreferences___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1194
+ * property nreferences:
+ * '''number of :term:`reference` sequences in the file.'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return self.samfile.header.n_targets
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile__buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile__buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
-static PyObject *__pyx_pf_9csamtools_7Samfile__buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_fields = 0;
- PyObject *__pyx_v_record = 0;
- PyObject *__pyx_v_line;
- PyObject *__pyx_v_key;
+static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- int __pyx_t_7;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildLine");
- __Pyx_TraceCall("_buildLine", __pyx_f[0], 1078);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_fields = values[0];
- __pyx_v_record = values[1];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_fields = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_record = PyTuple_GET_ITEM(__pyx_args, 1);
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile._buildLine");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_line = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_key = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1194);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1082
+ /* "csamtools.pyx":1195
+ * '''number of :term:`reference` sequences in the file.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self.samfile.header.n_targets
*
- * # TODO: add checking for field and sort order
- * line = ["@%s" % record ] # <<<<<<<<<<<<<<
- * if record == "CO":
- * line.append( fields )
- */
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_50), __pyx_v_record); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_v_line));
- __pyx_v_line = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1083
- * # TODO: add checking for field and sort order
- * line = ["@%s" % record ]
- * if record == "CO": # <<<<<<<<<<<<<<
- * line.append( fields )
- * else:
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_3) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1084
- * line = ["@%s" % record ]
- * if record == "CO":
- * line.append( fields ) # <<<<<<<<<<<<<<
- * else:
- * # write fields of the specification
- */
- if (unlikely(__pyx_v_line == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = PyList_Append(((PyObject *)__pyx_v_line), __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_88), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- /*else*/ {
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1087
- * else:
- * # write fields of the specification
- * for key in VALID_HEADER_ORDER[record]: # <<<<<<<<<<<<<<
- * if key in fields:
- * line.append( "%s:%s" % (key, str(fields[key])))
+ /* "csamtools.pyx":1196
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return self.samfile.header.n_targets # <<<<<<<<<<<<<<
+ *
+ * property references:
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetItem(__pyx_t_2, __pyx_v_record); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
- __pyx_t_5 = 0; __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2);
- } else {
- __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- }
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_2))) {
- if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_2))) {
- if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
- } else {
- __pyx_t_1 = PyIter_Next(__pyx_t_2);
- if (!__pyx_t_1) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_1);
- }
- __Pyx_DECREF(__pyx_v_key);
- __pyx_v_key = __pyx_t_1;
- __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1088
- * # write fields of the specification
- * for key in VALID_HEADER_ORDER[record]:
- * if key in fields: # <<<<<<<<<<<<<<
- * line.append( "%s:%s" % (key, str(fields[key])))
- * # write user fields
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.nreferences.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_10references___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1200
+ * property references:
+ * """tuple with the names of :term:`reference` sequences."""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * t = []
*/
- __pyx_t_3 = ((PySequence_Contains(__pyx_v_fields, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1089
- * for key in VALID_HEADER_ORDER[record]:
- * if key in fields:
- * line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
- * # write user fields
- * for key in fields:
+static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_v_t = NULL;
+ long __pyx_v_x;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int32_t __pyx_t_5;
+ int __pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1200);
+
+ /* "csamtools.pyx":1201
+ * """tuple with the names of :term:`reference` sequences."""
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets:
*/
- if (unlikely(__pyx_v_line == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)&PyString_Type)), __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_v_key);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_key);
- __Pyx_GIVEREF(__pyx_v_key);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_51), __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_4 = PyList_Append(((PyObject *)__pyx_v_line), ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- goto __pyx_L9;
- }
- __pyx_L9:;
- }
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1091
- * line.append( "%s:%s" % (key, str(fields[key])))
- * # write user fields
- * for key in fields: # <<<<<<<<<<<<<<
- * if not key.isupper():
- * line.append( "%s:%s" % (key, str(fields[key])))
+ /* "csamtools.pyx":1202
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * t = [] # <<<<<<<<<<<<<<
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ * t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
*/
- if (PyList_CheckExact(__pyx_v_fields) || PyTuple_CheckExact(__pyx_v_fields)) {
- __pyx_t_5 = 0; __pyx_t_2 = __pyx_v_fields; __Pyx_INCREF(__pyx_t_2);
- } else {
- __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_fields); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- }
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_2))) {
- if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_2))) {
- if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
- } else {
- __pyx_t_1 = PyIter_Next(__pyx_t_2);
- if (!__pyx_t_1) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_1);
- }
- __Pyx_DECREF(__pyx_v_key);
- __pyx_v_key = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1092
- * # write user fields
- * for key in fields:
- * if not key.isupper(): # <<<<<<<<<<<<<<
- * line.append( "%s:%s" % (key, str(fields[key])))
- *
+ /* "csamtools.pyx":1203
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
+ * t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
+ * return tuple(t)
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = (!__pyx_t_3);
- if (__pyx_t_7) {
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1093
- * for key in fields:
- * if not key.isupper():
- * line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1204
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ * t.append( _charptr_to_str(self.samfile.header.target_name[x]) ) # <<<<<<<<<<<<<<
+ * return tuple(t)
*
- * return "\t".join( line )
*/
- if (unlikely(__pyx_v_line == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)&PyString_Type)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_key);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_key);
- __Pyx_GIVEREF(__pyx_v_key);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_51), __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = PyList_Append(((PyObject *)__pyx_v_line), ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- goto __pyx_L12;
- }
- __pyx_L12:;
- }
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- __pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1095
- * line.append( "%s:%s" % (key, str(fields[key])))
- *
- * return "\t".join( line ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1205
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ * t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
+ * return tuple(t) # <<<<<<<<<<<<<<
*
- * cdef bam_header_t * _buildHeader( self, new_header ):
+ * property lengths:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_v_line));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_line));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_line));
- __pyx_t_1 = PyObject_Call(__pyx_t_2, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("csamtools.Samfile._buildLine");
+ __Pyx_AddTraceback("csamtools.Samfile.references.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_line);
- __Pyx_DECREF(__pyx_v_key);
+ __Pyx_XDECREF(__pyx_v_t);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1097
- * return "\t".join( line )
- *
- * cdef bam_header_t * _buildHeader( self, new_header ): # <<<<<<<<<<<<<<
- * '''return a new header built from a dictionary in *new_header*.
- *
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_7lengths___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1211
+ * :attr:`pysam.Samfile.references`
+ * """
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * t = []
*/
-static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_new_header) {
- PyObject *__pyx_v_lines;
- bam_header_t *__pyx_v_dest;
- PyObject *__pyx_v_record;
- PyObject *__pyx_v_ttype;
- PyObject *__pyx_v_data;
- PyObject *__pyx_v_fields;
- PyObject *__pyx_v_text;
- PyObject *__pyx_v_seqs;
+static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
- PyObject *__pyx_v_seqname;
- PyObject *__pyx_v_seqlen;
- bam_header_t *__pyx_r;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- Py_ssize_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- int __pyx_t_7;
- Py_ssize_t __pyx_t_8;
- PyObject *__pyx_t_9 = NULL;
- char *__pyx_t_10;
- PyObject *__pyx_t_11 = NULL;
- int32_t __pyx_t_12;
- uint32_t __pyx_t_13;
+ int32_t __pyx_t_5;
+ int __pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildHeader");
- __Pyx_TraceCall("_buildHeader", __pyx_f[0], 1097);
- __pyx_v_lines = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_record = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_ttype = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_data = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_fields = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_text = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_seqs = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_seqname = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_seqlen = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1103
- * '''
- *
- * lines = [] # <<<<<<<<<<<<<<
- *
- * # check if hash exists
- */
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_lines));
- __pyx_v_lines = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1110
- * cdef bam_header_t * dest
- *
- * dest = bam_header_init() # <<<<<<<<<<<<<<
- *
- * for record in VALID_HEADERS:
- */
- __pyx_v_dest = bam_header_init();
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1211);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1112
- * dest = bam_header_init()
- *
- * for record in VALID_HEADERS: # <<<<<<<<<<<<<<
- * if record in new_header:
- * ttype = VALID_HEADER_TYPES[record]
+ /* "csamtools.pyx":1212
+ * """
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
- __pyx_t_2 = 0; __pyx_t_3 = __pyx_t_1; __Pyx_INCREF(__pyx_t_3);
- } else {
- __pyx_t_2 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- }
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_3))) {
- if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_3))) {
- if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
- } else {
- __pyx_t_1 = PyIter_Next(__pyx_t_3);
- if (!__pyx_t_1) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_1);
- }
- __Pyx_DECREF(__pyx_v_record);
- __pyx_v_record = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_90), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1113
- *
- * for record in VALID_HEADERS:
- * if record in new_header: # <<<<<<<<<<<<<<
- * ttype = VALID_HEADER_TYPES[record]
- * data = new_header[record]
+ /* "csamtools.pyx":1213
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * t = [] # <<<<<<<<<<<<<<
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ * t.append( self.samfile.header.target_len[x] )
*/
- __pyx_t_4 = ((PySequence_Contains(__pyx_v_new_header, __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_4) {
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1114
- * for record in VALID_HEADERS:
- * if record in new_header:
- * ttype = VALID_HEADER_TYPES[record] # <<<<<<<<<<<<<<
- * data = new_header[record]
- * if type( data ) != type( ttype() ):
+ /* "csamtools.pyx":1214
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
+ * t.append( self.samfile.header.target_len[x] )
+ * return tuple(t)
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_ttype);
- __pyx_v_ttype = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1115
- * if record in new_header:
- * ttype = VALID_HEADER_TYPES[record]
- * data = new_header[record] # <<<<<<<<<<<<<<
- * if type( data ) != type( ttype() ):
- * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
+ /* "csamtools.pyx":1215
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ * t.append( self.samfile.header.target_len[x] ) # <<<<<<<<<<<<<<
+ * return tuple(t)
+ *
*/
- __pyx_t_5 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_v_data);
- __pyx_v_data = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((__pyx_v_self->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1116
- * ttype = VALID_HEADER_TYPES[record]
- * data = new_header[record]
- * if type( data ) != type( ttype() ): # <<<<<<<<<<<<<<
- * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
- * if type( data ) == types.DictType:
+ /* "csamtools.pyx":1216
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ * t.append( self.samfile.header.target_len[x] )
+ * return tuple(t) # <<<<<<<<<<<<<<
+ *
+ * property mapped:
*/
- __pyx_t_5 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_5)), Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_4) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1117
- * data = new_header[record]
- * if type( data ) != type( ttype() ):
- * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) ) # <<<<<<<<<<<<<<
- * if type( data ) == types.DictType:
- * lines.append( self._buildLine( data, record ) )
- */
- __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(__pyx_v_record);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_record);
- __Pyx_GIVEREF(__pyx_v_record);
- __Pyx_INCREF(((PyObject *)Py_TYPE(__pyx_v_data)));
- PyTuple_SET_ITEM(__pyx_t_5, 1, ((PyObject *)Py_TYPE(__pyx_v_data)));
- __Pyx_GIVEREF(((PyObject *)Py_TYPE(__pyx_v_data)));
- __Pyx_INCREF(((PyObject *)Py_TYPE(__pyx_t_1)));
- PyTuple_SET_ITEM(__pyx_t_5, 2, ((PyObject *)Py_TYPE(__pyx_t_1)));
- __Pyx_GIVEREF(((PyObject *)Py_TYPE(__pyx_t_1)));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_52), __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.lengths.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_t);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1118
- * if type( data ) != type( ttype() ):
- * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
- * if type( data ) == types.DictType: # <<<<<<<<<<<<<<
- * lines.append( self._buildLine( data, record ) )
- * else:
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__types); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__DictType); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_4) {
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_6mapped___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1119
- * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
- * if type( data ) == types.DictType:
- * lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
- * else:
- * for fields in new_header[record]:
+/* "csamtools.pyx":1221
+ * """total number of mapped reads in file.
+ * """
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*/
- if (unlikely(__pyx_v_lines == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(__pyx_v_data);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_data);
- __Pyx_GIVEREF(__pyx_v_data);
- __Pyx_INCREF(__pyx_v_record);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_record);
- __Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_6 = PyObject_Call(__pyx_t_1, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_7 = PyList_Append(((PyObject *)__pyx_v_lines), __pyx_t_6); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L7;
- }
- /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1121
- * lines.append( self._buildLine( data, record ) )
- * else:
- * for fields in new_header[record]: # <<<<<<<<<<<<<<
- * lines.append( self._buildLine( fields, record ) )
- *
- */
- __pyx_t_6 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if (PyList_CheckExact(__pyx_t_6) || PyTuple_CheckExact(__pyx_t_6)) {
- __pyx_t_8 = 0; __pyx_t_5 = __pyx_t_6; __Pyx_INCREF(__pyx_t_5);
- } else {
- __pyx_t_8 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- }
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_5))) {
- if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_5)) break;
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_5))) {
- if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_8); __Pyx_INCREF(__pyx_t_6); __pyx_t_8++;
- } else {
- __pyx_t_6 = PyIter_Next(__pyx_t_5);
- if (!__pyx_t_6) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_6);
- }
- __Pyx_DECREF(__pyx_v_fields);
- __pyx_v_fields = __pyx_t_6;
- __pyx_t_6 = 0;
+static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ int __pyx_v_tid;
+ uint32_t __pyx_v_total;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int32_t __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1221);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1122
- * else:
- * for fields in new_header[record]:
- * lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1222
+ * """
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*
- * text = "\n".join(lines) + "\n"
*/
- if (unlikely(__pyx_v_lines == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_fields);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
- __Pyx_GIVEREF(__pyx_v_fields);
- __Pyx_INCREF(__pyx_v_record);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
- __Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_9 = PyObject_Call(__pyx_t_6, __pyx_t_1, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_7 = PyList_Append(((PyObject *)__pyx_v_lines), __pyx_t_9); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- }
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- }
- __pyx_L7:;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_91), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1124
- * lines.append( self._buildLine( fields, record ) )
+ /* "csamtools.pyx":1223
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
*
- * text = "\n".join(lines) + "\n" # <<<<<<<<<<<<<<
- * if dest.text != NULL: free( dest.text )
- * dest.text = <char*>calloc( len(text), sizeof(char))
+ * cdef int tid
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_v_lines));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_lines));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_lines));
- __pyx_t_9 = PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Add(__pyx_t_9, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_4 = (!__pyx_v_self->isbam);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_93), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1125
+ /* "csamtools.pyx":1226
*
- * text = "\n".join(lines) + "\n"
- * if dest.text != NULL: free( dest.text ) # <<<<<<<<<<<<<<
- * dest.text = <char*>calloc( len(text), sizeof(char))
- * dest.l_text = len(text)
+ * cdef int tid
+ * cdef uint32_t total = 0 # <<<<<<<<<<<<<<
+ * for tid from 0 <= tid < self.samfile.header.n_targets:
+ * total += pysam_get_mapped( self.index, tid )
*/
- __pyx_t_4 = (__pyx_v_dest->text != NULL);
- if (__pyx_t_4) {
- free(__pyx_v_dest->text);
- goto __pyx_L10;
- }
- __pyx_L10:;
+ __pyx_v_total = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1126
- * text = "\n".join(lines) + "\n"
- * if dest.text != NULL: free( dest.text )
- * dest.text = <char*>calloc( len(text), sizeof(char)) # <<<<<<<<<<<<<<
- * dest.l_text = len(text)
- * strncpy( dest.text, text, dest.l_text )
+ /* "csamtools.pyx":1227
+ * cdef int tid
+ * cdef uint32_t total = 0
+ * for tid from 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
+ * total += pysam_get_mapped( self.index, tid )
+ * return total
*/
- __pyx_t_2 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest->text = ((char *)calloc(__pyx_t_2, (sizeof(char))));
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1127
- * if dest.text != NULL: free( dest.text )
- * dest.text = <char*>calloc( len(text), sizeof(char))
- * dest.l_text = len(text) # <<<<<<<<<<<<<<
- * strncpy( dest.text, text, dest.l_text )
+ /* "csamtools.pyx":1228
+ * cdef uint32_t total = 0
+ * for tid from 0 <= tid < self.samfile.header.n_targets:
+ * total += pysam_get_mapped( self.index, tid ) # <<<<<<<<<<<<<<
+ * return total
*
*/
- __pyx_t_2 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest->l_text = __pyx_t_2;
+ __pyx_v_total = (__pyx_v_total + pysam_get_mapped(__pyx_v_self->index, __pyx_v_tid));
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1128
- * dest.text = <char*>calloc( len(text), sizeof(char))
- * dest.l_text = len(text)
- * strncpy( dest.text, text, dest.l_text ) # <<<<<<<<<<<<<<
- *
- * # collect targets
- */
- __pyx_t_10 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy(__pyx_v_dest->text, __pyx_t_10, __pyx_v_dest->l_text);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1131
+ /* "csamtools.pyx":1229
+ * for tid from 0 <= tid < self.samfile.header.n_targets:
+ * total += pysam_get_mapped( self.index, tid )
+ * return total # <<<<<<<<<<<<<<
*
- * # collect targets
- * if "SQ" in new_header: # <<<<<<<<<<<<<<
- * seqs = []
- * for fields in new_header["SQ"]:
- */
- __pyx_t_4 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1132
- * # collect targets
- * if "SQ" in new_header:
- * seqs = [] # <<<<<<<<<<<<<<
- * for fields in new_header["SQ"]:
- * try:
- */
- __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __Pyx_DECREF(((PyObject *)__pyx_v_seqs));
- __pyx_v_seqs = __pyx_t_5;
- __pyx_t_5 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1133
- * if "SQ" in new_header:
- * seqs = []
- * for fields in new_header["SQ"]: # <<<<<<<<<<<<<<
- * try:
- * seqs.append( (fields["SN"], fields["LN"] ) )
- */
- __pyx_t_5 = PyObject_GetItem(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- if (PyList_CheckExact(__pyx_t_5) || PyTuple_CheckExact(__pyx_t_5)) {
- __pyx_t_2 = 0; __pyx_t_9 = __pyx_t_5; __Pyx_INCREF(__pyx_t_9);
- } else {
- __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- }
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_9))) {
- if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_5 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_9))) {
- if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
- } else {
- __pyx_t_5 = PyIter_Next(__pyx_t_9);
- if (!__pyx_t_5) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_5);
- }
- __Pyx_DECREF(__pyx_v_fields);
- __pyx_v_fields = __pyx_t_5;
- __pyx_t_5 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1134
- * seqs = []
- * for fields in new_header["SQ"]:
- * try: # <<<<<<<<<<<<<<
- * seqs.append( (fields["SN"], fields["LN"] ) )
- * except KeyError:
- */
- {
- PyObject *__pyx_save_exc_type, *__pyx_save_exc_value, *__pyx_save_exc_tb;
- __Pyx_ExceptionSave(&__pyx_save_exc_type, &__pyx_save_exc_value, &__pyx_save_exc_tb);
- __Pyx_XGOTREF(__pyx_save_exc_type);
- __Pyx_XGOTREF(__pyx_save_exc_value);
- __Pyx_XGOTREF(__pyx_save_exc_tb);
- /*try:*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1135
- * for fields in new_header["SQ"]:
- * try:
- * seqs.append( (fields["SN"], fields["LN"] ) ) # <<<<<<<<<<<<<<
- * except KeyError:
- * raise KeyError( "incomplete sequence information in '%s'" % str(fields))
+ * property unmapped:
*/
- if (unlikely(__pyx_v_seqs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;}
- }
- __pyx_t_5 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_5 = 0;
- __pyx_t_3 = 0;
- __pyx_t_7 = PyList_Append(((PyObject *)__pyx_v_seqs), __pyx_t_1); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- }
- __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0;
- __Pyx_XDECREF(__pyx_save_exc_value); __pyx_save_exc_value = 0;
- __Pyx_XDECREF(__pyx_save_exc_tb); __pyx_save_exc_tb = 0;
- goto __pyx_L21_try_end;
- __pyx_L14_error:;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_total); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1136
- * try:
- * seqs.append( (fields["SN"], fields["LN"] ) )
- * except KeyError: # <<<<<<<<<<<<<<
- * raise KeyError( "incomplete sequence information in '%s'" % str(fields))
- *
- */
- __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
- if (__pyx_t_7) {
- __Pyx_AddTraceback("csamtools.Samfile._buildHeader");
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_3, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.mapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1137
- * seqs.append( (fields["SN"], fields["LN"] ) )
- * except KeyError:
- * raise KeyError( "incomplete sequence information in '%s'" % str(fields)) # <<<<<<<<<<<<<<
- *
- * dest.n_targets = len(seqs)
- */
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_v_fields);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields);
- __Pyx_GIVEREF(__pyx_v_fields);
- __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)&PyString_Type)), __pyx_t_6, NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_53), __pyx_t_11); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
- PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_KeyError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- goto __pyx_L15_exception_handled;
- }
- __pyx_L16_except_error:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- goto __pyx_L1_error;
- __pyx_L15_exception_handled:;
- __Pyx_XGIVEREF(__pyx_save_exc_type);
- __Pyx_XGIVEREF(__pyx_save_exc_value);
- __Pyx_XGIVEREF(__pyx_save_exc_tb);
- __Pyx_ExceptionReset(__pyx_save_exc_type, __pyx_save_exc_value, __pyx_save_exc_tb);
- __pyx_L21_try_end:;
- }
- }
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_8unmapped___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1139
- * raise KeyError( "incomplete sequence information in '%s'" % str(fields))
- *
- * dest.n_targets = len(seqs) # <<<<<<<<<<<<<<
- * dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
- * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
+/* "csamtools.pyx":1234
+ * """total number of unmapped reads in file.
+ * """
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
*/
- if (unlikely(__pyx_v_seqs == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs));
- __pyx_v_dest->n_targets = __pyx_t_2;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1140
- *
- * dest.n_targets = len(seqs)
- * dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) ) # <<<<<<<<<<<<<<
- * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
- *
- */
- __pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *))));
+static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ int __pyx_v_tid;
+ uint32_t __pyx_v_total;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int32_t __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1234);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1141
- * dest.n_targets = len(seqs)
- * dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
- * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) ) # <<<<<<<<<<<<<<
- *
- * for x from 0 <= x < dest.n_targets:
+ /* "csamtools.pyx":1235
+ * """
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
+ * cdef int tid
*/
- __pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t))));
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_94), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1143
- * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
- *
- * for x from 0 <= x < dest.n_targets: # <<<<<<<<<<<<<<
- * seqname, seqlen = seqs[x]
- * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
+ /* "csamtools.pyx":1236
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
+ * cdef int tid
+ * cdef uint32_t total = 0
*/
- __pyx_t_12 = __pyx_v_dest->n_targets;
- for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_12; __pyx_v_x++) {
+ __pyx_t_4 = (!__pyx_v_self->isbam);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_96), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1144
- *
- * for x from 0 <= x < dest.n_targets:
- * seqname, seqlen = seqs[x] # <<<<<<<<<<<<<<
- * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
- * strncpy( dest.target_name[x], seqname, len(seqname) + 1 )
+ /* "csamtools.pyx":1238
+ * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
+ * cdef int tid
+ * cdef uint32_t total = 0 # <<<<<<<<<<<<<<
+ * for tid from 0 <= tid < self.samfile.header.n_targets:
+ * total += pysam_get_unmapped( self.index, tid )
*/
- __pyx_t_9 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- if (PyTuple_CheckExact(__pyx_t_9) && likely(PyTuple_GET_SIZE(__pyx_t_9) == 2)) {
- PyObject* tuple = __pyx_t_9;
- __pyx_t_5 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_5);
- __pyx_t_3 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_v_seqname);
- __pyx_v_seqname = __pyx_t_5;
- __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_v_seqlen);
- __pyx_v_seqlen = __pyx_t_3;
- __pyx_t_3 = 0;
- } else {
- __pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_UnpackItem(__pyx_t_1, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_1, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_EndUnpack(__pyx_t_1, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_seqname);
- __pyx_v_seqname = __pyx_t_5;
- __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_v_seqlen);
- __pyx_v_seqlen = __pyx_t_3;
- __pyx_t_3 = 0;
- }
+ __pyx_v_total = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1145
- * for x from 0 <= x < dest.n_targets:
- * seqname, seqlen = seqs[x]
- * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) ) # <<<<<<<<<<<<<<
- * strncpy( dest.target_name[x], seqname, len(seqname) + 1 )
- * dest.target_len[x] = seqlen
+ /* "csamtools.pyx":1239
+ * cdef int tid
+ * cdef uint32_t total = 0
+ * for tid from 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
+ * total += pysam_get_unmapped( self.index, tid )
+ * # get unmapped reads without coordinates
*/
- __pyx_t_2 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_dest->target_name[__pyx_v_x]) = ((char *)calloc((__pyx_t_2 + 1), (sizeof(char))));
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1146
- * seqname, seqlen = seqs[x]
- * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
- * strncpy( dest.target_name[x], seqname, len(seqname) + 1 ) # <<<<<<<<<<<<<<
- * dest.target_len[x] = seqlen
- *
+ /* "csamtools.pyx":1240
+ * cdef uint32_t total = 0
+ * for tid from 0 <= tid < self.samfile.header.n_targets:
+ * total += pysam_get_unmapped( self.index, tid ) # <<<<<<<<<<<<<<
+ * # get unmapped reads without coordinates
+ * total += pysam_get_unmapped( self.index, -1 )
*/
- __pyx_t_10 = PyBytes_AsString(__pyx_v_seqname); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy((__pyx_v_dest->target_name[__pyx_v_x]), __pyx_t_10, (__pyx_t_2 + 1));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, __pyx_v_tid));
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1147
- * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
- * strncpy( dest.target_name[x], seqname, len(seqname) + 1 )
- * dest.target_len[x] = seqlen # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1242
+ * total += pysam_get_unmapped( self.index, tid )
+ * # get unmapped reads without coordinates
+ * total += pysam_get_unmapped( self.index, -1 ) # <<<<<<<<<<<<<<
+ * return total
*
- * return dest
*/
- __pyx_t_13 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_seqlen); if (unlikely((__pyx_t_13 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_dest->target_len[__pyx_v_x]) = __pyx_t_13;
- }
- goto __pyx_L11;
- }
- __pyx_L11:;
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, -1));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1149
- * dest.target_len[x] = seqlen
- *
- * return dest # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1243
+ * # get unmapped reads without coordinates
+ * total += pysam_get_unmapped( self.index, -1 )
+ * return total # <<<<<<<<<<<<<<
*
- * ###############################################################
+ * property text:
*/
- __pyx_r = __pyx_v_dest;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_total); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
- __pyx_r = 0;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_WriteUnraisable("csamtools.Samfile._buildHeader");
- __pyx_r = 0;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_lines);
- __Pyx_DECREF(__pyx_v_record);
- __Pyx_DECREF(__pyx_v_ttype);
- __Pyx_DECREF(__pyx_v_data);
- __Pyx_DECREF(__pyx_v_fields);
- __Pyx_DECREF(__pyx_v_text);
- __Pyx_DECREF(__pyx_v_seqs);
- __Pyx_DECREF(__pyx_v_seqname);
- __Pyx_DECREF(__pyx_v_seqlen);
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1159
- * ## Possible solutions: deprecate or open new file handle
- * ###############################################################
- * def __iter__(self): # <<<<<<<<<<<<<<
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_4text___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1247
+ * property text:
+ * '''full contents of the :term:`sam file` header as a string.'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile___iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1159);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1247);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1160
- * ###############################################################
- * def __iter__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- * return self
+ /* "csamtools.pyx":1248
+ * '''full contents of the :term:`sam file` header as a string.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1161
- * def __iter__(self):
- * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- * return self # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1249
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) # <<<<<<<<<<<<<<
*
- * cdef bam1_t * getCurrent( self ):
+ * property header:
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(__pyx_v_self->samfile->header->text, __pyx_v_self->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__iter__");
+ __Pyx_AddTraceback("csamtools.Samfile.text.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1163
- * return self
- *
- * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
- * return self.b
- *
- */
-
-static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
- bam1_t *__pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1163);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1164
- *
- * cdef bam1_t * getCurrent( self ):
- * return self.b # <<<<<<<<<<<<<<
- *
- * cdef int cnext(self):
- */
- __pyx_r = __pyx_v_self->b;
- goto __pyx_L0;
-
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_6header___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1166
- * return self.b
- *
- * cdef int cnext(self): # <<<<<<<<<<<<<<
- * '''
- * cversion of iterator. Used by :class:`pysam.Samfile.IteratorColumn`.
- */
-
-static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
- int __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1166);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1171
+/* "csamtools.pyx":1255
+ * a two-level dictionary.
* '''
- * cdef int ret
- * return samread(self.samfile, self.b) # <<<<<<<<<<<<<<
- *
- * def __next__(self):
- */
- __pyx_r = samread(__pyx_v_self->samfile, __pyx_v_self->b);
- goto __pyx_L0;
-
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1173
- * return samread(self.samfile, self.b)
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
*
- * def __next__(self): # <<<<<<<<<<<<<<
- * """
- * python version of next().
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile___next__[] = "\n python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile___next__;
-static PyObject *__pyx_pf_9csamtools_7Samfile___next__(PyObject *__pyx_v_self) {
- int __pyx_v_ret;
+static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_v_result = NULL;
+ PyObject *__pyx_v_t = NULL;
+ PyObject *__pyx_v_line = NULL;
+ PyObject *__pyx_v_fields = NULL;
+ PyObject *__pyx_v_record = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_field = NULL;
+ PyObject *__pyx_v_key = NULL;
+ PyObject *__pyx_v_value = NULL;
+ PyObject *__pyx_v_sq = NULL;
+ PyObject *__pyx_v_ref = NULL;
+ PyObject *__pyx_v_length = NULL;
PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1173);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1178
- * """
- * cdef int ret
- * ret = samread(self.samfile, self.b) # <<<<<<<<<<<<<<
- * if (ret > 0):
- * return makeAlignedRead( self.b )
- */
- __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1179
- * cdef int ret
- * ret = samread(self.samfile, self.b)
- * if (ret > 0): # <<<<<<<<<<<<<<
- * return makeAlignedRead( self.b )
- * else:
- */
- __pyx_t_1 = (__pyx_v_ret > 0);
- if (__pyx_t_1) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1180
- * ret = samread(self.samfile, self.b)
- * if (ret > 0):
- * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
- * else:
- * raise StopIteration
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1182
- * return makeAlignedRead( self.b )
- * else:
- * raise StopIteration # <<<<<<<<<<<<<<
- *
- * ##-------------------------------------------------------------------
- */
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L5:;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__next__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1234
- * cdef int owns_samfile
- *
- * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
-
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- int __pyx_v_tid;
- int __pyx_v_beg;
- int __pyx_v_end;
- int __pyx_v_reopen;
- PyObject *__pyx_v_mode;
- PyObject *__pyx_v_store;
- int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
- char *__pyx_t_5;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ Py_ssize_t __pyx_t_10;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ PyObject *__pyx_t_12 = NULL;
+ PyObject *(*__pyx_t_13)(PyObject *);
+ int __pyx_t_14;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1234);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[5] = {0,0,0,0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg);
- if (likely(values[2])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[3])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- case 4:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
- if (value) { values[4] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_beg = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_beg == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- if (values[4]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else {
- __pyx_v_reopen = ((int)1);
- }
- } else {
- __pyx_v_reopen = ((int)1);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 5:
- __pyx_v_reopen = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 4)); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 4:
- __pyx_v_end = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 3)); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_beg = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 2)); if (unlikely((__pyx_v_beg == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_tid = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
- break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_mode = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_store = Py_None; __Pyx_INCREF(Py_None);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1255);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1236
- * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
- *
- * if not samfile._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
+ /* "csamtools.pyx":1256
+ * '''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
+ * result = {}
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1237
- *
- * if not samfile._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- *
- * if not samfile._hasIndex():
- */
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1239
- * raise ValueError( "I/O operation on closed file" )
+ /* "csamtools.pyx":1258
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
*
- * if not samfile._hasIndex(): # <<<<<<<<<<<<<<
- * raise ValueError( "no index available for iteration" )
+ * result = {} # <<<<<<<<<<<<<<
*
+ * if self.samfile.header.text != NULL:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1240
- *
- * if not samfile._hasIndex():
- * raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1260
+ * result = {}
*
- * # makes sure that samfile stays alive as long as the
+ * if self.samfile.header.text != NULL: # <<<<<<<<<<<<<<
+ * # convert to python string (note: call self.text to create 0-terminated string)
+ * t = self.text
+ */
+ __pyx_t_4 = (__pyx_v_self->samfile->header->text != NULL);
+ if (__pyx_t_4) {
+
+ /* "csamtools.pyx":1262
+ * if self.samfile.header.text != NULL:
+ * # convert to python string (note: call self.text to create 0-terminated string)
+ * t = self.text # <<<<<<<<<<<<<<
+ * for line in t.split("\n"):
+ * if not line.strip(): continue
+ */
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":1263
+ * # convert to python string (note: call self.text to create 0-terminated string)
+ * t = self.text
+ * for line in t.split("\n"): # <<<<<<<<<<<<<<
+ * if not line.strip(): continue
+ * assert line.startswith("@"), "header line without '@': '%s'" % line
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_t, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_54));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_54));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_54));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
+ if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ }
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
- }
- __pyx_L7:;
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
+ } else {
+ __pyx_t_1 = __pyx_t_6(__pyx_t_2);
+ if (unlikely(!__pyx_t_1)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_1);
+ }
+ __Pyx_XDECREF(__pyx_v_line);
+ __pyx_v_line = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1244
- * # makes sure that samfile stays alive as long as the
- * # iterator is alive
- * self.samfile = samfile # <<<<<<<<<<<<<<
- *
- * if samfile.isbam: mode = "rb"
+ /* "csamtools.pyx":1264
+ * t = self.text
+ * for line in t.split("\n"):
+ * if not line.strip(): continue # <<<<<<<<<<<<<<
+ * assert line.startswith("@"), "header line without '@': '%s'" % line
+ * fields = line[1:].split("\t")
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile = __pyx_v_samfile;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1246
- * self.samfile = samfile
- *
- * if samfile.isbam: mode = "rb" # <<<<<<<<<<<<<<
- * else: mode = "r"
- *
- */
- if (__pyx_v_samfile->isbam) {
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__rb);
- goto __pyx_L8;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1247
- *
- * if samfile.isbam: mode = "rb"
- * else: mode = "r" # <<<<<<<<<<<<<<
- *
- * # reopen the file - note that this makes the iterator
- */
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__r);
- }
- __pyx_L8:;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
+ goto __pyx_L5_continue;
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1251
- * # reopen the file - note that this makes the iterator
- * # slow and causes pileup to slow down significantly.
- * if reopen: # <<<<<<<<<<<<<<
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
+ /* "csamtools.pyx":1265
+ * for line in t.split("\n"):
+ * if not line.strip(): continue
+ * assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
+ * fields = line[1:].split("\t")
+ * record = fields[0]
*/
- if (__pyx_v_reopen) {
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_101), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (unlikely(!__pyx_t_3)) {
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_102), __pyx_v_line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1252
- * # slow and causes pileup to slow down significantly.
- * if reopen:
- * store = StderrStore() # <<<<<<<<<<<<<<
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
+ /* "csamtools.pyx":1266
+ * if not line.strip(): continue
+ * assert line.startswith("@"), "header line without '@': '%s'" % line
+ * fields = line[1:].split("\t") # <<<<<<<<<<<<<<
+ * record = fields[0]
+ * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_store);
- __pyx_v_store = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_103), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_fields);
+ __pyx_v_fields = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1253
- * if reopen:
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
- * store.release()
- * assert self.fp != NULL
+ /* "csamtools.pyx":1267
+ * assert line.startswith("@"), "header line without '@': '%s'" % line
+ * fields = line[1:].split("\t")
+ * record = fields[0] # <<<<<<<<<<<<<<
+ * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
+ *
*/
- __pyx_t_5 = PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_fields, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_v_record);
+ __pyx_v_record = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1254
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release() # <<<<<<<<<<<<<<
- * assert self.fp != NULL
- * self.owns_samfile = True
+ /* "csamtools.pyx":1268
+ * fields = line[1:].split("\t")
+ * record = fields[0]
+ * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line) # <<<<<<<<<<<<<<
+ *
+ * # treat comments
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (unlikely(!__pyx_t_3)) {
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __Pyx_INCREF(__pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_line);
+ __Pyx_GIVEREF(__pyx_v_line);
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_104), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1255
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
- * assert self.fp != NULL # <<<<<<<<<<<<<<
- * self.owns_samfile = True
- * else:
+ /* "csamtools.pyx":1271
+ *
+ * # treat comments
+ * if record == "CO": # <<<<<<<<<<<<<<
+ * if record not in result: result[record] = []
+ * result[record].append( "\t".join( fields[1:] ) )
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1255; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1256
- * store.release()
- * assert self.fp != NULL
- * self.owns_samfile = True # <<<<<<<<<<<<<<
- * else:
- * self.fp = self.samfile.samfile
+ /* "csamtools.pyx":1272
+ * # treat comments
+ * if record == "CO":
+ * if record not in result: result[record] = [] # <<<<<<<<<<<<<<
+ * result[record].append( "\t".join( fields[1:] ) )
+ * continue
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L9;
- }
- /*else*/ {
+ __pyx_t_3 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
+ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1258
- * self.owns_samfile = True
- * else:
- * self.fp = self.samfile.samfile # <<<<<<<<<<<<<<
- * self.owns_samfile = False
+ /* "csamtools.pyx":1273
+ * if record == "CO":
+ * if record not in result: result[record] = []
+ * result[record].append( "\t".join( fields[1:] ) ) # <<<<<<<<<<<<<<
+ * continue
*
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->samfile;
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_7, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1259
- * else:
- * self.fp = self.samfile.samfile
- * self.owns_samfile = False # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1274
+ * if record not in result: result[record] = []
+ * result[record].append( "\t".join( fields[1:] ) )
+ * continue # <<<<<<<<<<<<<<
*
- * self.retval = 0
+ * # the following is clumsy as generators do not work?
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 0;
- }
- __pyx_L9:;
+ goto __pyx_L5_continue;
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1261
- * self.owns_samfile = False
+ /* "csamtools.pyx":1277
*
- * self.retval = 0 # <<<<<<<<<<<<<<
- *
- * self.iter = bam_iter_query(self.samfile.index,
+ * # the following is clumsy as generators do not work?
+ * x = {} # <<<<<<<<<<<<<<
+ * for field in fields[1:]:
+ * key, value = field.split(":",1)
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval = 0;
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __Pyx_XDECREF(((PyObject *)__pyx_v_x));
+ __pyx_v_x = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1263
- * self.retval = 0
- *
- * self.iter = bam_iter_query(self.samfile.index, # <<<<<<<<<<<<<<
- * tid,
- * beg,
+ /* "csamtools.pyx":1278
+ * # the following is clumsy as generators do not work?
+ * x = {}
+ * for field in fields[1:]: # <<<<<<<<<<<<<<
+ * key, value = field.split(":",1)
+ * # uppercase keys must be valid
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter = bam_iter_query(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
+ __pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_10 = 0;
+ __pyx_t_11 = NULL;
+ } else {
+ __pyx_t_10 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_11 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ for (;;) {
+ if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
+ } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
+ } else {
+ __pyx_t_9 = __pyx_t_11(__pyx_t_8);
+ if (unlikely(!__pyx_t_9)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_9);
+ }
+ __Pyx_XDECREF(__pyx_v_field);
+ __pyx_v_field = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1267
- * beg,
- * end)
- * self.b = bam_init1() # <<<<<<<<<<<<<<
- *
- * def __iter__(self):
+ /* "csamtools.pyx":1279
+ * x = {}
+ * for field in fields[1:]:
+ * key, value = field.split(":",1) # <<<<<<<<<<<<<<
+ * # uppercase keys must be valid
+ * # lowercase are permitted for user fields
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b = bam_init1();
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_mode);
- __Pyx_DECREF(__pyx_v_store);
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_field, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_106), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
+ PyObject* sequence = __pyx_t_7;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_12 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
+ index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L12_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
+ goto __pyx_L13_unpacking_done;
+ __pyx_L12_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L13_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_key);
+ __pyx_v_key = __pyx_t_9;
+ __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_1;
+ __pyx_t_1 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1269
- * self.b = bam_init1()
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
- *
+ /* "csamtools.pyx":1282
+ * # uppercase keys must be valid
+ * # lowercase are permitted for user fields
+ * if key in VALID_HEADER_FIELDS[record]: # <<<<<<<<<<<<<<
+ * x[key] = VALID_HEADER_FIELDS[record][key](value)
+ * elif not key.isupper():
*/
+ __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_record); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_3) {
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion___iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1269);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1270
- *
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
- *
- * cdef bam1_t * getCurrent( self ):
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":1283
+ * # lowercase are permitted for user fields
+ * if key in VALID_HEADER_FIELDS[record]:
+ * x[key] = VALID_HEADER_FIELDS[record][key](value) # <<<<<<<<<<<<<<
+ * elif not key.isupper():
+ * x[key] = value
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_key); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
+ __Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ goto __pyx_L14;
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1272
- * return self
- *
- * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
- * return self.b
- *
+ /* "csamtools.pyx":1284
+ * if key in VALID_HEADER_FIELDS[record]:
+ * x[key] = VALID_HEADER_FIELDS[record][key](value)
+ * elif not key.isupper(): # <<<<<<<<<<<<<<
+ * x[key] = value
+ * else:
*/
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
-static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
- bam1_t *__pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1272);
+ /* "csamtools.pyx":1285
+ * x[key] = VALID_HEADER_FIELDS[record][key](value)
+ * elif not key.isupper():
+ * x[key] = value # <<<<<<<<<<<<<<
+ * else:
+ * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
+ */
+ if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L14;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1273
- *
- * cdef bam1_t * getCurrent( self ):
- * return self.b # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1287
+ * x[key] = value
+ * else:
+ * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) ) # <<<<<<<<<<<<<<
*
- * cdef int cnext(self):
+ * if VALID_HEADER_TYPES[record] == dict:
*/
- __pyx_r = __pyx_v_self->b;
- goto __pyx_L0;
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
+ __Pyx_GIVEREF(__pyx_v_key);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_107), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_9));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_9, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L14:;
+ }
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":1289
+ * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
+ *
+ * if VALID_HEADER_TYPES[record] == dict: # <<<<<<<<<<<<<<
+ * if record in result:
+ * raise ValueError( "multiple '%s' lines are not permitted" % record )
+ */
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyDict_Type))), Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_4) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1275
- * return self.b
+ /* "csamtools.pyx":1290
*
- * cdef int cnext(self): # <<<<<<<<<<<<<<
- * '''cversion of iterator. Used by IteratorColumn'''
- * self.retval = bam_iter_read( self.fp.x.bam,
+ * if VALID_HEADER_TYPES[record] == dict:
+ * if record in result: # <<<<<<<<<<<<<<
+ * raise ValueError( "multiple '%s' lines are not permitted" % record )
+ * result[record] = x
*/
+ __pyx_t_4 = ((PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_4) {
-static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
- int __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1275);
+ /* "csamtools.pyx":1291
+ * if VALID_HEADER_TYPES[record] == dict:
+ * if record in result:
+ * raise ValueError( "multiple '%s' lines are not permitted" % record ) # <<<<<<<<<<<<<<
+ * result[record] = x
+ * elif VALID_HEADER_TYPES[record] == list:
+ */
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L16;
+ }
+ __pyx_L16:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1277
- * cdef int cnext(self):
- * '''cversion of iterator. Used by IteratorColumn'''
- * self.retval = bam_iter_read( self.fp.x.bam, # <<<<<<<<<<<<<<
- * self.iter,
- * self.b)
+ /* "csamtools.pyx":1292
+ * if record in result:
+ * raise ValueError( "multiple '%s' lines are not permitted" % record )
+ * result[record] = x # <<<<<<<<<<<<<<
+ * elif VALID_HEADER_TYPES[record] == list:
+ * if record not in result: result[record] = []
*/
- __pyx_v_self->retval = bam_iter_read(__pyx_v_self->fp->x.bam, __pyx_v_self->iter, __pyx_v_self->b);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L15;
+ }
- __pyx_r = 0;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":1293
+ * raise ValueError( "multiple '%s' lines are not permitted" % record )
+ * result[record] = x
+ * elif VALID_HEADER_TYPES[record] == list: # <<<<<<<<<<<<<<
+ * if record not in result: result[record] = []
+ * result[record].append( x )
+ */
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyList_Type))), Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_4) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1281
- * self.b)
+ /* "csamtools.pyx":1294
+ * result[record] = x
+ * elif VALID_HEADER_TYPES[record] == list:
+ * if record not in result: result[record] = [] # <<<<<<<<<<<<<<
+ * result[record].append( x )
*
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
- * """
*/
+ __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_4) {
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ goto __pyx_L17;
+ }
+ __pyx_L17:;
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_17IteratorRowRegion___next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__;
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion___next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1281);
+ /* "csamtools.pyx":1295
+ * elif VALID_HEADER_TYPES[record] == list:
+ * if record not in result: result[record] = []
+ * result[record].append( x ) # <<<<<<<<<<<<<<
+ *
+ * # if there are no SQ lines in the header, add the reference names
+ */
+ __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_8, ((PyObject *)__pyx_v_x)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ goto __pyx_L15;
+ }
+ __pyx_L15:;
+ __pyx_L5_continue:;
+ }
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1284
- * """python version of next().
- * """
- * self.cnext() # <<<<<<<<<<<<<<
- * if self.retval < 0: raise StopIteration
- * return makeAlignedRead( self.b )
+ /* "csamtools.pyx":1303
+ * # SQ lines, the SQ information is not part of the textual header and thus
+ * # are missing from the output. See issue 84.
+ * if "SQ" not in result: # <<<<<<<<<<<<<<
+ * sq = []
+ * for ref, length in zip( self.references, self.lengths ):
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1285
- * """
- * self.cnext()
- * if self.retval < 0: raise StopIteration # <<<<<<<<<<<<<<
- * return makeAlignedRead( self.b )
+ /* "csamtools.pyx":1304
+ * # are missing from the output. See issue 84.
+ * if "SQ" not in result:
+ * sq = [] # <<<<<<<<<<<<<<
+ * for ref, length in zip( self.references, self.lengths ):
+ * sq.append( {'LN': length, 'SN': ref } )
+ */
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_sq = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":1305
+ * if "SQ" not in result:
+ * sq = []
+ * for ref, length in zip( self.references, self.lengths ): # <<<<<<<<<<<<<<
+ * sq.append( {'LN': length, 'SN': ref } )
+ * result["SQ"] = sq
+ */
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_2 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
+ __pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_5 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_6 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
+ } else {
+ __pyx_t_9 = __pyx_t_6(__pyx_t_8);
+ if (unlikely(!__pyx_t_9)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_9);
+ }
+ if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
+ PyObject* sequence = __pyx_t_9;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L21_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L21_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_1), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L22_unpacking_done;
+ __pyx_L21_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L22_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_ref);
+ __pyx_v_ref = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_v_length);
+ __pyx_v_length = __pyx_t_7;
+ __pyx_t_7 = 0;
+
+ /* "csamtools.pyx":1306
+ * sq = []
+ * for ref, length in zip( self.references, self.lengths ):
+ * sq.append( {'LN': length, 'SN': ref } ) # <<<<<<<<<<<<<<
+ * result["SQ"] = sq
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval < 0);
- if (__pyx_t_1) {
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__LN), __pyx_v_length) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__SN), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyList_Append(__pyx_v_sq, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+
+ /* "csamtools.pyx":1307
+ * for ref, length in zip( self.references, self.lengths ):
+ * sq.append( {'LN': length, 'SN': ref } )
+ * result["SQ"] = sq # <<<<<<<<<<<<<<
+ *
+ * return result
+ */
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_sq)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L18;
+ }
+ __pyx_L18:;
+ goto __pyx_L4;
}
- __pyx_L5:;
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1286
- * self.cnext()
- * if self.retval < 0: raise StopIteration
- * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1309
+ * result["SQ"] = sq
*
- * def __dealloc__(self):
+ * return result # <<<<<<<<<<<<<<
+ *
+ * def _buildLine( self, fields, record ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_v_result));
+ __pyx_r = ((PyObject *)__pyx_v_result);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowRegion.__next__");
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_12);
+ __Pyx_AddTraceback("csamtools.Samfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_result);
+ __Pyx_XDECREF(__pyx_v_t);
+ __Pyx_XDECREF(__pyx_v_line);
+ __Pyx_XDECREF(__pyx_v_fields);
+ __Pyx_XDECREF(__pyx_v_record);
+ __Pyx_XDECREF(__pyx_v_x);
+ __Pyx_XDECREF(__pyx_v_field);
+ __Pyx_XDECREF(__pyx_v_key);
+ __Pyx_XDECREF(__pyx_v_value);
+ __Pyx_XDECREF(__pyx_v_sq);
+ __Pyx_XDECREF(__pyx_v_ref);
+ __Pyx_XDECREF(__pyx_v_length);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1288
- * return makeAlignedRead( self.b )
- *
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * bam_destroy1(self.b)
- * if self.owns_samfile: samclose( self.fp )
- */
-
-static void __pyx_pf_9csamtools_17IteratorRowRegion___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_17IteratorRowRegion___dealloc__(PyObject *__pyx_v_self) {
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1288);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1289
- *
- * def __dealloc__(self):
- * bam_destroy1(self.b) # <<<<<<<<<<<<<<
- * if self.owns_samfile: samclose( self.fp )
- *
- */
- bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1290
- * def __dealloc__(self):
- * bam_destroy1(self.b)
- * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
- *
- * cdef class IteratorRowAll(IteratorRow):
- */
- if (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp);
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1307
- * cdef int owns_samfile
- *
- * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
-
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- int __pyx_v_reopen;
- PyObject *__pyx_v_mode;
- PyObject *__pyx_v_store;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1307);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_38_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
+static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_fields = 0;
+ PyObject *__pyx_v_record = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_buildLine (wrapper)", 0);
+ {
PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
- if (value) { values[1] = value; kw_args--; }
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
}
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- if (values[1]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
+ goto __pyx_L5_argtuple_error;
} else {
- __pyx_v_reopen = ((int)1);
- }
- } else {
- __pyx_v_reopen = ((int)1);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: __pyx_v_reopen = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 1: __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
- break;
- default: goto __pyx_L5_argtuple_error;
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
}
+ __pyx_v_fields = values[0];
+ __pyx_v_record = values[1];
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__");
+ __Pyx_AddTraceback("csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
- return -1;
+ return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_v_mode = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_store = Py_None; __Pyx_INCREF(Py_None);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_38_buildLine(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_fields, __pyx_v_record);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1309
- * def __cinit__(self, Samfile samfile, int reopen = True ):
+/* "csamtools.pyx":1311
+ * return result
*
- * if not samfile._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
+ * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
+ * '''build a header line from *fields* dictionary for *record*'''
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1310
- *
- * if not samfile._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record) {
+ PyObject *__pyx_v_line = NULL;
+ PyObject *__pyx_v_key = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_buildLine", 0);
+ __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311);
+
+ /* "csamtools.pyx":1315
*
- * if samfile.isbam: mode = "rb"
+ * # TODO: add checking for field and sort order
+ * line = ["@%s" % record ] # <<<<<<<<<<<<<<
+ * # comment
+ * if record == "CO":
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_109), __pyx_v_record); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_v_line = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1312
- * raise ValueError( "I/O operation on closed file" )
- *
- * if samfile.isbam: mode = "rb" # <<<<<<<<<<<<<<
- * else: mode = "r"
- *
+ /* "csamtools.pyx":1317
+ * line = ["@%s" % record ]
+ * # comment
+ * if record == "CO": # <<<<<<<<<<<<<<
+ * line.append( fields )
+ * # user tags
*/
- if (__pyx_v_samfile->isbam) {
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__rb);
- goto __pyx_L7;
- }
- /*else*/ {
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1313
- *
- * if samfile.isbam: mode = "rb"
- * else: mode = "r" # <<<<<<<<<<<<<<
- *
- * # reopen the file to avoid iterator conflict
+ /* "csamtools.pyx":1318
+ * # comment
+ * if record == "CO":
+ * line.append( fields ) # <<<<<<<<<<<<<<
+ * # user tags
+ * elif record.islower():
*/
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__r);
+ __pyx_t_4 = PyList_Append(__pyx_v_line, __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1316
- *
- * # reopen the file to avoid iterator conflict
- * if reopen: # <<<<<<<<<<<<<<
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
+ /* "csamtools.pyx":1320
+ * line.append( fields )
+ * # user tags
+ * elif record.islower(): # <<<<<<<<<<<<<<
+ * for key in sorted(fields):
+ * line.append( "%s:%s" % (key, str(fields[key])))
*/
- if (__pyx_v_reopen) {
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__islower); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1317
- * # reopen the file to avoid iterator conflict
- * if reopen:
- * store = StderrStore() # <<<<<<<<<<<<<<
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
+ /* "csamtools.pyx":1321
+ * # user tags
+ * elif record.islower():
+ * for key in sorted(fields): # <<<<<<<<<<<<<<
+ * line.append( "%s:%s" % (key, str(fields[key])))
+ * # defined tags
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_store);
- __pyx_v_store = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1318
- * if reopen:
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
- * store.release()
- * assert self.fp != NULL
- */
- __pyx_t_5 = PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1319
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release() # <<<<<<<<<<<<<<
- * assert self.fp != NULL
- * self.owns_samfile = True
- */
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_v_fields);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
+ __Pyx_GIVEREF(__pyx_v_fields);
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
+ __pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ }
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else {
+ __pyx_t_2 = __pyx_t_6(__pyx_t_1);
+ if (unlikely(!__pyx_t_2)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_2);
+ }
+ __Pyx_XDECREF(__pyx_v_key);
+ __pyx_v_key = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1320
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
- * assert self.fp != NULL # <<<<<<<<<<<<<<
- * self.owns_samfile = True
+ /* "csamtools.pyx":1322
+ * elif record.islower():
+ * for key in sorted(fields):
+ * line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
+ * # defined tags
* else:
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
+ __Pyx_GIVEREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
}
- #endif
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1321
- * store.release()
- * assert self.fp != NULL
- * self.owns_samfile = True # <<<<<<<<<<<<<<
- * else:
- * self.fp = samfile.samfile
- */
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L8;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L3;
}
/*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1323
- * self.owns_samfile = True
+ /* "csamtools.pyx":1326
* else:
- * self.fp = samfile.samfile # <<<<<<<<<<<<<<
- * self.owns_samfile = False
- *
+ * # write fields of the specification
+ * for key in VALID_HEADER_ORDER[record]: # <<<<<<<<<<<<<<
+ * if key in fields:
+ * line.append( "%s:%s" % (key, str(fields[key])))
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
+ __pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else {
+ __pyx_t_2 = __pyx_t_6(__pyx_t_1);
+ if (unlikely(!__pyx_t_2)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_2);
+ }
+ __Pyx_XDECREF(__pyx_v_key);
+ __pyx_v_key = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1324
- * else:
- * self.fp = samfile.samfile
- * self.owns_samfile = False # <<<<<<<<<<<<<<
- *
- * # allocate memory for alignment
+ /* "csamtools.pyx":1327
+ * # write fields of the specification
+ * for key in VALID_HEADER_ORDER[record]:
+ * if key in fields: # <<<<<<<<<<<<<<
+ * line.append( "%s:%s" % (key, str(fields[key])))
+ * # write user fields
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 0;
- }
- __pyx_L8:;
+ __pyx_t_3 = ((PySequence_Contains(__pyx_v_fields, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1327
- *
- * # allocate memory for alignment
- * self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
- *
- * def __iter__(self):
+ /* "csamtools.pyx":1328
+ * for key in VALID_HEADER_ORDER[record]:
+ * if key in fields:
+ * line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
+ * # write user fields
+ * for key in fields:
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_mode);
- __Pyx_DECREF(__pyx_v_store);
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
+ __Pyx_GIVEREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1329
- * self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
+ /* "csamtools.pyx":1330
+ * line.append( "%s:%s" % (key, str(fields[key])))
+ * # write user fields
+ * for key in fields: # <<<<<<<<<<<<<<
+ * if not key.isupper():
+ * line.append( "%s:%s" % (key, str(fields[key])))
+ */
+ if (PyList_CheckExact(__pyx_v_fields) || PyTuple_CheckExact(__pyx_v_fields)) {
+ __pyx_t_1 = __pyx_v_fields; __Pyx_INCREF(__pyx_t_1); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_fields); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ }
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else {
+ __pyx_t_2 = __pyx_t_6(__pyx_t_1);
+ if (unlikely(!__pyx_t_2)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_2);
+ }
+ __Pyx_XDECREF(__pyx_v_key);
+ __pyx_v_key = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":1331
+ * # write user fields
+ * for key in fields:
+ * if not key.isupper(): # <<<<<<<<<<<<<<
+ * line.append( "%s:%s" % (key, str(fields[key])))
*
*/
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_8 = (!__pyx_t_3);
+ if (__pyx_t_8) {
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll___iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1329);
+ /* "csamtools.pyx":1332
+ * for key in fields:
+ * if not key.isupper():
+ * line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
+ *
+ * return "\t".join( line )
+ */
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
+ __Pyx_GIVEREF(__pyx_v_key);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ goto __pyx_L11;
+ }
+ __pyx_L11:;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1330
+ /* "csamtools.pyx":1334
+ * line.append( "%s:%s" % (key, str(fields[key])))
*
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
+ * return "\t".join( line ) # <<<<<<<<<<<<<<
*
- * cdef bam1_t * getCurrent( self ):
+ * cdef bam_header_t * _buildHeader( self, new_header ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(((PyObject *)__pyx_v_line));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_line));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_line));
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_AddTraceback("csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_line);
+ __Pyx_XDECREF(__pyx_v_key);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1332
- * return self
+/* "csamtools.pyx":1336
+ * return "\t".join( line )
*
- * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
- * return self.b
+ * cdef bam_header_t * _buildHeader( self, new_header ): # <<<<<<<<<<<<<<
+ * '''return a new header built from a dictionary in *new_header*.
*
*/
-static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
- bam1_t *__pyx_r;
+static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_new_header) {
+ PyObject *__pyx_v_lines = NULL;
+ bam_header_t *__pyx_v_dest;
+ PyObject *__pyx_v_record = NULL;
+ PyObject *__pyx_v_ttype = NULL;
+ PyObject *__pyx_v_data = NULL;
+ PyObject *__pyx_v_fields = NULL;
+ PyObject *__pyx_v_text = NULL;
+ PyObject *__pyx_v_btext = 0;
+ PyObject *__pyx_v_bseqname = 0;
+ PyObject *__pyx_v_seqs = NULL;
+ long __pyx_v_x;
+ PyObject *__pyx_v_seqname = NULL;
+ PyObject *__pyx_v_seqlen = NULL;
+ bam_header_t *__pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ Py_ssize_t __pyx_t_3;
+ PyObject *(*__pyx_t_4)(PyObject *);
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_8;
+ Py_ssize_t __pyx_t_9;
+ PyObject *(*__pyx_t_10)(PyObject *);
+ PyObject *__pyx_t_11 = NULL;
+ PyObject *(*__pyx_t_12)(PyObject *);
+ char *__pyx_t_13;
+ PyObject *__pyx_t_14 = NULL;
+ PyObject *__pyx_t_15 = NULL;
+ PyObject *__pyx_t_16 = NULL;
+ int __pyx_t_17;
+ PyObject *__pyx_t_18 = NULL;
+ int32_t __pyx_t_19;
+ uint32_t __pyx_t_20;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1332);
+ __Pyx_RefNannySetupContext("_buildHeader", 0);
+ __Pyx_TraceCall("_buildHeader", __pyx_f[0], 1336);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1333
+ /* "csamtools.pyx":1342
+ * '''
*
- * cdef bam1_t * getCurrent( self ):
- * return self.b # <<<<<<<<<<<<<<
+ * lines = [] # <<<<<<<<<<<<<<
*
- * cdef int cnext(self):
+ * # check if hash exists
*/
- __pyx_r = __pyx_v_self->b;
- goto __pyx_L0;
-
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_lines = __pyx_t_1;
+ __pyx_t_1 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1335
- * return self.b
+ /* "csamtools.pyx":1349
+ * cdef bam_header_t * dest
*
- * cdef int cnext(self): # <<<<<<<<<<<<<<
- * '''cversion of iterator. Used by IteratorColumn'''
- * cdef int ret
- */
-
-static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
- int __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1335);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1338
- * '''cversion of iterator. Used by IteratorColumn'''
- * cdef int ret
- * return samread(self.fp, self.b) # <<<<<<<<<<<<<<
+ * dest = bam_header_init() # <<<<<<<<<<<<<<
*
- * def __next__(self):
+ * # first: defined tags
*/
- __pyx_r = samread(__pyx_v_self->fp, __pyx_v_self->b);
- goto __pyx_L0;
-
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_v_dest = bam_header_init();
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1340
- * return samread(self.fp, self.b)
- *
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
+ /* "csamtools.pyx":1352
*
+ * # first: defined tags
+ * for record in VALID_HEADERS: # <<<<<<<<<<<<<<
+ * if record in new_header:
+ * ttype = VALID_HEADER_TYPES[record]
*/
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
+ __pyx_t_4 = NULL;
+ } else {
+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ for (;;) {
+ if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+ } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+ } else {
+ __pyx_t_1 = __pyx_t_4(__pyx_t_2);
+ if (unlikely(!__pyx_t_1)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_1);
+ }
+ __Pyx_XDECREF(__pyx_v_record);
+ __pyx_v_record = __pyx_t_1;
+ __pyx_t_1 = 0;
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorRowAll___next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__;
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll___next__(PyObject *__pyx_v_self) {
- int __pyx_v_ret;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1340);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1346
- * """
- * cdef int ret
- * ret = samread(self.fp, self.b) # <<<<<<<<<<<<<<
- * if (ret > 0):
- * return makeAlignedRead( self.b )
+ /* "csamtools.pyx":1353
+ * # first: defined tags
+ * for record in VALID_HEADERS:
+ * if record in new_header: # <<<<<<<<<<<<<<
+ * ttype = VALID_HEADER_TYPES[record]
+ * data = new_header[record]
*/
- __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp, ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1347
- * cdef int ret
- * ret = samread(self.fp, self.b)
- * if (ret > 0): # <<<<<<<<<<<<<<
- * return makeAlignedRead( self.b )
- * else:
+ /* "csamtools.pyx":1354
+ * for record in VALID_HEADERS:
+ * if record in new_header:
+ * ttype = VALID_HEADER_TYPES[record] # <<<<<<<<<<<<<<
+ * data = new_header[record]
+ * if type( data ) != type( ttype() ):
*/
- __pyx_t_1 = (__pyx_v_ret > 0);
- if (__pyx_t_1) {
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_v_ttype);
+ __pyx_v_ttype = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1348
- * ret = samread(self.fp, self.b)
- * if (ret > 0):
- * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
- * else:
- * raise StopIteration
+ /* "csamtools.pyx":1355
+ * if record in new_header:
+ * ttype = VALID_HEADER_TYPES[record]
+ * data = new_header[record] # <<<<<<<<<<<<<<
+ * if type( data ) != type( ttype() ):
+ * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_t_6 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_v_data);
+ __pyx_v_data = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1350
- * return makeAlignedRead( self.b )
- * else:
- * raise StopIteration # <<<<<<<<<<<<<<
- *
- * def __dealloc__(self):
+ /* "csamtools.pyx":1356
+ * ttype = VALID_HEADER_TYPES[record]
+ * data = new_header[record]
+ * if type( data ) != type( ttype() ): # <<<<<<<<<<<<<<
+ * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
+ * if type( data ) is dict:
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L5:;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAll.__next__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_6 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_6)), Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_5) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1352
- * raise StopIteration
- *
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * bam_destroy1(self.b)
- * if self.owns_samfile: samclose( self.fp )
+ /* "csamtools.pyx":1357
+ * data = new_header[record]
+ * if type( data ) != type( ttype() ):
+ * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) ) # <<<<<<<<<<<<<<
+ * if type( data ) is dict:
+ * lines.append( self._buildLine( data, record ) )
*/
+ __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __Pyx_INCREF(((PyObject *)Py_TYPE(__pyx_v_data)));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)Py_TYPE(__pyx_v_data)));
+ __Pyx_GIVEREF(((PyObject *)Py_TYPE(__pyx_v_data)));
+ __Pyx_INCREF(((PyObject *)Py_TYPE(__pyx_t_1)));
+ PyTuple_SET_ITEM(__pyx_t_6, 2, ((PyObject *)Py_TYPE(__pyx_t_1)));
+ __Pyx_GIVEREF(((PyObject *)Py_TYPE(__pyx_t_1)));
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_111), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
-static void __pyx_pf_9csamtools_14IteratorRowAll___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_14IteratorRowAll___dealloc__(PyObject *__pyx_v_self) {
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1352);
+ /* "csamtools.pyx":1358
+ * if type( data ) != type( ttype() ):
+ * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
+ * if type( data ) is dict: # <<<<<<<<<<<<<<
+ * lines.append( self._buildLine( data, record ) )
+ * else:
+ */
+ __pyx_t_5 = (((PyObject *)Py_TYPE(__pyx_v_data)) == ((PyObject *)((PyObject*)(&PyDict_Type))));
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1353
- *
- * def __dealloc__(self):
- * bam_destroy1(self.b) # <<<<<<<<<<<<<<
- * if self.owns_samfile: samclose( self.fp )
- *
+ /* "csamtools.pyx":1359
+ * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
+ * if type( data ) is dict:
+ * lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
+ * else:
+ * for fields in new_header[record]:
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_data);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_data);
+ __Pyx_GIVEREF(__pyx_v_data);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ goto __pyx_L7;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1354
- * def __dealloc__(self):
- * bam_destroy1(self.b)
- * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1361
+ * lines.append( self._buildLine( data, record ) )
+ * else:
+ * for fields in new_header[record]: # <<<<<<<<<<<<<<
+ * lines.append( self._buildLine( fields, record ) )
*
- * cdef class IteratorRowAllRefs(IteratorRow):
*/
- if (((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp);
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
+ __pyx_t_6 = __pyx_t_7; __Pyx_INCREF(__pyx_t_6); __pyx_t_9 = 0;
+ __pyx_t_10 = NULL;
+ } else {
+ __pyx_t_9 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_10 = Py_TYPE(__pyx_t_6)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ for (;;) {
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_6)) {
+ if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_6)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_6)) {
+ if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
+ } else {
+ __pyx_t_7 = __pyx_t_10(__pyx_t_6);
+ if (unlikely(!__pyx_t_7)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_7);
+ }
+ __Pyx_XDECREF(__pyx_v_fields);
+ __pyx_v_fields = __pyx_t_7;
+ __pyx_t_7 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1363
- * cdef IteratorRowRegion rowiter
+ /* "csamtools.pyx":1362
+ * else:
+ * for fields in new_header[record]:
+ * lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
*
- * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
- * assert samfile._isOpen()
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ * # then: user tags (lower case), sorted alphabetically
*/
-
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1363);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_fields);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
+ __Pyx_GIVEREF(__pyx_v_fields);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __pyx_t_11 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_11); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ }
+ __pyx_L7:;
+ goto __pyx_L5;
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
+ __pyx_L5:;
}
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1364
+ /* "csamtools.pyx":1365
*
- * def __cinit__(self, Samfile samfile):
- * assert samfile._isOpen() # <<<<<<<<<<<<<<
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
- * self.samfile = samfile
+ * # then: user tags (lower case), sorted alphabetically
+ * for record, data in sorted(new_header.items()): # <<<<<<<<<<<<<<
+ * if record in VALID_HEADERS: continue
+ * if type( data ) is dict:
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_new_header, __pyx_n_s__items); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(!__pyx_t_3)) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1365
- * def __cinit__(self, Samfile samfile):
- * assert samfile._isOpen()
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
- * self.samfile = samfile
- * self.tid = -1
- */
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = (!__pyx_t_3);
- if (__pyx_t_4) {
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ if (PyList_CheckExact(__pyx_t_6) || PyTuple_CheckExact(__pyx_t_6)) {
+ __pyx_t_2 = __pyx_t_6; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
+ __pyx_t_4 = NULL;
+ } else {
+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
- __pyx_L6:;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (;;) {
+ if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ } else {
+ __pyx_t_6 = __pyx_t_4(__pyx_t_2);
+ if (unlikely(!__pyx_t_6)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_6);
+ }
+ if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
+ PyObject* sequence = __pyx_t_6;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_11 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_11 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_11);
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_12 = Py_TYPE(__pyx_t_7)->tp_iternext;
+ index = 0; __pyx_t_11 = __pyx_t_12(__pyx_t_7); if (unlikely(!__pyx_t_11)) goto __pyx_L12_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_11);
+ index = 1; __pyx_t_1 = __pyx_t_12(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ goto __pyx_L13_unpacking_done;
+ __pyx_L12_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L13_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_record);
+ __pyx_v_record = __pyx_t_11;
+ __pyx_t_11 = 0;
+ __Pyx_XDECREF(__pyx_v_data);
+ __pyx_v_data = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1366
- * assert samfile._isOpen()
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
- * self.samfile = samfile # <<<<<<<<<<<<<<
- * self.tid = -1
- *
+ /* "csamtools.pyx":1366
+ * # then: user tags (lower case), sorted alphabetically
+ * for record, data in sorted(new_header.items()):
+ * if record in VALID_HEADERS: continue # <<<<<<<<<<<<<<
+ * if type( data ) is dict:
+ * lines.append( self._buildLine( data, record ) )
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile = __pyx_v_samfile;
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_5 = ((PySequence_Contains(__pyx_t_6, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_5) {
+ goto __pyx_L10_continue;
+ goto __pyx_L14;
+ }
+ __pyx_L14:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1367
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
- * self.samfile = samfile
- * self.tid = -1 # <<<<<<<<<<<<<<
- *
- * def nextiter(self):
+ /* "csamtools.pyx":1367
+ * for record, data in sorted(new_header.items()):
+ * if record in VALID_HEADERS: continue
+ * if type( data ) is dict: # <<<<<<<<<<<<<<
+ * lines.append( self._buildLine( data, record ) )
+ * else:
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = -1;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_5 = (((PyObject *)Py_TYPE(__pyx_v_data)) == ((PyObject *)((PyObject*)(&PyDict_Type))));
+ if (__pyx_t_5) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1369
- * self.tid = -1
- *
- * def nextiter(self): # <<<<<<<<<<<<<<
- * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
- *
+ /* "csamtools.pyx":1368
+ * if record in VALID_HEADERS: continue
+ * if type( data ) is dict:
+ * lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
+ * else:
+ * for fields in new_header[record]:
*/
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_data);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_data);
+ __Pyx_GIVEREF(__pyx_v_data);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __pyx_t_11 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_11); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L15;
+ }
+ /*else*/ {
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorRowAllRefs_nextiter[] = "IteratorRowAllRefs.nextiter(self)";
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("nextiter");
- __Pyx_TraceCall("nextiter", __pyx_f[0], 1369);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1370
- *
- * def nextiter(self):
- * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1370
+ * lines.append( self._buildLine( data, record ) )
+ * else:
+ * for fields in new_header[record]: # <<<<<<<<<<<<<<
+ * lines.append( self._buildLine( fields, record ) )
*
- * def __iter__(self):
*/
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_536870912);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_int_536870912);
- __Pyx_GIVEREF(__pyx_int_536870912);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ if (PyList_CheckExact(__pyx_t_11) || PyTuple_CheckExact(__pyx_t_11)) {
+ __pyx_t_1 = __pyx_t_11; __Pyx_INCREF(__pyx_t_1); __pyx_t_9 = 0;
+ __pyx_t_10 = NULL;
+ } else {
+ __pyx_t_9 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_10 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ for (;;) {
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
+ } else {
+ __pyx_t_11 = __pyx_t_10(__pyx_t_1);
+ if (unlikely(!__pyx_t_11)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_11);
+ }
+ __Pyx_XDECREF(__pyx_v_fields);
+ __pyx_v_fields = __pyx_t_11;
+ __pyx_t_11 = 0;
+
+ /* "csamtools.pyx":1371
+ * else:
+ * for fields in new_header[record]:
+ * lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
+ *
+ * text = "\n".join(lines) + "\n"
+ */
+ __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_fields);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields);
+ __Pyx_GIVEREF(__pyx_v_fields);
+ __Pyx_INCREF(__pyx_v_record);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_record);
+ __Pyx_GIVEREF(__pyx_v_record);
+ __pyx_t_7 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ }
+ __pyx_L15:;
+ __pyx_L10_continue:;
+ }
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":1373
+ * lines.append( self._buildLine( fields, record ) )
+ *
+ * text = "\n".join(lines) + "\n" # <<<<<<<<<<<<<<
+ * if dest.text != NULL: free( dest.text )
+ * dest.text = <char*>calloc( len(text), sizeof(char))
+ */
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)__pyx_v_lines));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_lines));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_lines));
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter));
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Add(__pyx_t_7, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_v_text = __pyx_t_1;
__pyx_t_1 = 0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.nextiter");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1372
- * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
+ /* "csamtools.pyx":1374
*
+ * text = "\n".join(lines) + "\n"
+ * if dest.text != NULL: free( dest.text ) # <<<<<<<<<<<<<<
+ * dest.text = <char*>calloc( len(text), sizeof(char))
+ * dest.l_text = len(text)
*/
+ __pyx_t_5 = (__pyx_v_dest->text != NULL);
+ if (__pyx_t_5) {
+ free(__pyx_v_dest->text);
+ goto __pyx_L18;
+ }
+ __pyx_L18:;
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs___iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1372);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1373
- *
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
- *
- * def __next__(self):
+ /* "csamtools.pyx":1375
+ * text = "\n".join(lines) + "\n"
+ * if dest.text != NULL: free( dest.text )
+ * dest.text = <char*>calloc( len(text), sizeof(char)) # <<<<<<<<<<<<<<
+ * dest.l_text = len(text)
+ * cdef bytes btext = text.encode('ascii')
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
- goto __pyx_L0;
+ __pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest->text = ((char *)calloc(__pyx_t_3, (sizeof(char))));
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":1376
+ * if dest.text != NULL: free( dest.text )
+ * dest.text = <char*>calloc( len(text), sizeof(char))
+ * dest.l_text = len(text) # <<<<<<<<<<<<<<
+ * cdef bytes btext = text.encode('ascii')
+ * strncpy( dest.text, btext, dest.l_text )
+ */
+ __pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest->l_text = __pyx_t_3;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1375
- * return self
- *
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
+ /* "csamtools.pyx":1377
+ * dest.text = <char*>calloc( len(text), sizeof(char))
+ * dest.l_text = len(text)
+ * cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<<
+ * strncpy( dest.text, btext, dest.l_text )
*
*/
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_text, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!(likely(PyBytes_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_btext = ((PyObject*)__pyx_t_7);
+ __pyx_t_7 = 0;
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorRowAllRefs___next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__;
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs___next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1375);
+ /* "csamtools.pyx":1378
+ * dest.l_text = len(text)
+ * cdef bytes btext = text.encode('ascii')
+ * strncpy( dest.text, btext, dest.l_text ) # <<<<<<<<<<<<<<
+ *
+ * cdef bytes bseqname
+ */
+ __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_btext)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy(__pyx_v_dest->text, __pyx_t_13, __pyx_v_dest->l_text);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1381
- * """
- * # Create an initial iterator
- * if self.tid==-1: # <<<<<<<<<<<<<<
- * if not self.samfile.nreferences:
- * raise StopIteration
+ /* "csamtools.pyx":1382
+ * cdef bytes bseqname
+ * # collect targets
+ * if "SQ" in new_header: # <<<<<<<<<<<<<<
+ * seqs = []
+ * for fields in new_header["SQ"]:
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid == -1);
- if (__pyx_t_1) {
+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1382
- * # Create an initial iterator
- * if self.tid==-1:
- * if not self.samfile.nreferences: # <<<<<<<<<<<<<<
- * raise StopIteration
- * self.tid = 0
+ /* "csamtools.pyx":1383
+ * # collect targets
+ * if "SQ" in new_header:
+ * seqs = [] # <<<<<<<<<<<<<<
+ * for fields in new_header["SQ"]:
+ * try:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = (!__pyx_t_1);
- if (__pyx_t_3) {
+ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_v_seqs = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1383
- * if self.tid==-1:
- * if not self.samfile.nreferences:
- * raise StopIteration # <<<<<<<<<<<<<<
- * self.tid = 0
- * self.nextiter()
+ /* "csamtools.pyx":1384
+ * if "SQ" in new_header:
+ * seqs = []
+ * for fields in new_header["SQ"]: # <<<<<<<<<<<<<<
+ * try:
+ * seqs.append( (fields["SN"], fields["LN"] ) )
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
+ __pyx_t_1 = __pyx_t_7; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
+ __pyx_t_4 = NULL;
+ } else {
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
- __pyx_L6:;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ for (;;) {
+ if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else {
+ __pyx_t_7 = __pyx_t_4(__pyx_t_1);
+ if (unlikely(!__pyx_t_7)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_7);
+ }
+ __Pyx_XDECREF(__pyx_v_fields);
+ __pyx_v_fields = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1384
- * if not self.samfile.nreferences:
- * raise StopIteration
- * self.tid = 0 # <<<<<<<<<<<<<<
- * self.nextiter()
- *
+ /* "csamtools.pyx":1385
+ * seqs = []
+ * for fields in new_header["SQ"]:
+ * try: # <<<<<<<<<<<<<<
+ * seqs.append( (fields["SN"], fields["LN"] ) )
+ * except KeyError:
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = 0;
+ {
+ __Pyx_ExceptionSave(&__pyx_t_14, &__pyx_t_15, &__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_14);
+ __Pyx_XGOTREF(__pyx_t_15);
+ __Pyx_XGOTREF(__pyx_t_16);
+ /*try:*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1385
- * raise StopIteration
- * self.tid = 0
- * self.nextiter() # <<<<<<<<<<<<<<
- *
- * while 1:
+ /* "csamtools.pyx":1386
+ * for fields in new_header["SQ"]:
+ * try:
+ * seqs.append( (fields["SN"], fields["LN"] ) ) # <<<<<<<<<<<<<<
+ * except KeyError:
+ * raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_7 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_8 = PyList_Append(__pyx_v_seqs, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ goto __pyx_L29_try_end;
+ __pyx_L22_error:;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1387
- * self.nextiter()
- *
- * while 1: # <<<<<<<<<<<<<<
- * self.rowiter.cnext()
+ /* "csamtools.pyx":1387
+ * try:
+ * seqs.append( (fields["SN"], fields["LN"] ) )
+ * except KeyError: # <<<<<<<<<<<<<<
+ * raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*
*/
- while (1) {
- if (!1) break;
+ __pyx_t_17 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
+ if (__pyx_t_17) {
+ __Pyx_AddTraceback("csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1387; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_7);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1388
- *
- * while 1:
- * self.rowiter.cnext() # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1388
+ * seqs.append( (fields["SN"], fields["LN"] ) )
+ * except KeyError:
+ * raise KeyError( "incomplete sequence information in '%s'" % str(fields)) # <<<<<<<<<<<<<<
*
- * # If current iterator is not exhausted, return aligned read
+ * dest.n_targets = len(seqs)
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_INCREF(__pyx_v_fields);
+ PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_fields);
+ __Pyx_GIVEREF(__pyx_v_fields);
+ __pyx_t_18 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_18);
+ __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
+ __pyx_t_11 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_113), __pyx_t_18); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
+ __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
+ __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_18);
+ PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_11));
+ __pyx_t_11 = 0;
+ __pyx_t_11 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0;
+ __Pyx_Raise(__pyx_t_11, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ goto __pyx_L23_exception_handled;
+ }
+ __pyx_L24_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_14);
+ __Pyx_XGIVEREF(__pyx_t_15);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16);
+ goto __pyx_L1_error;
+ __pyx_L23_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_14);
+ __Pyx_XGIVEREF(__pyx_t_15);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16);
+ __pyx_L29_try_end:;
+ }
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1391
- *
- * # If current iterator is not exhausted, return aligned read
- * if self.rowiter.retval>0: # <<<<<<<<<<<<<<
- * return makeAlignedRead(self.rowiter.b)
+ /* "csamtools.pyx":1390
+ * raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*
+ * dest.n_targets = len(seqs) # <<<<<<<<<<<<<<
+ * dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
+ * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->retval > 0);
- if (__pyx_t_3) {
+ __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs));
+ __pyx_v_dest->n_targets = __pyx_t_3;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1392
- * # If current iterator is not exhausted, return aligned read
- * if self.rowiter.retval>0:
- * return makeAlignedRead(self.rowiter.b) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1391
+ *
+ * dest.n_targets = len(seqs)
+ * dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) ) # <<<<<<<<<<<<<<
+ * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*
- * self.tid += 1
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_r = __pyx_t_4;
- __pyx_t_4 = 0;
- goto __pyx_L0;
- goto __pyx_L9;
- }
- __pyx_L9:;
+ __pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *))));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1394
- * return makeAlignedRead(self.rowiter.b)
+ /* "csamtools.pyx":1392
+ * dest.n_targets = len(seqs)
+ * dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
+ * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) ) # <<<<<<<<<<<<<<
*
- * self.tid += 1 # <<<<<<<<<<<<<<
+ * for x from 0 <= x < dest.n_targets:
+ */
+ __pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t))));
+
+ /* "csamtools.pyx":1394
+ * dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*
- * # Otherwise, proceed to next reference or stop
+ * for x from 0 <= x < dest.n_targets: # <<<<<<<<<<<<<<
+ * seqname, seqlen = seqs[x]
+ * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid += 1;
+ __pyx_t_19 = __pyx_v_dest->n_targets;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_19; __pyx_v_x++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1397
+ /* "csamtools.pyx":1395
*
- * # Otherwise, proceed to next reference or stop
- * if self.tid<self.samfile.nreferences: # <<<<<<<<<<<<<<
- * self.nextiter()
- * else:
+ * for x from 0 <= x < dest.n_targets:
+ * seqname, seqlen = seqs[x] # <<<<<<<<<<<<<<
+ * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
+ * bseqname = seqname.encode('ascii')
*/
- __pyx_t_4 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_3) {
+ __pyx_t_1 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
+ PyObject* sequence = __pyx_t_1;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_6 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_12 = Py_TYPE(__pyx_t_6)->tp_iternext;
+ index = 0; __pyx_t_7 = __pyx_t_12(__pyx_t_6); if (unlikely(!__pyx_t_7)) goto __pyx_L34_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
+ index = 1; __pyx_t_2 = __pyx_t_12(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L34_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L35_unpacking_done;
+ __pyx_L34_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L35_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_seqname);
+ __pyx_v_seqname = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_seqlen);
+ __pyx_v_seqlen = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1398
- * # Otherwise, proceed to next reference or stop
- * if self.tid<self.samfile.nreferences:
- * self.nextiter() # <<<<<<<<<<<<<<
- * else:
- * raise StopIteration
+ /* "csamtools.pyx":1396
+ * for x from 0 <= x < dest.n_targets:
+ * seqname, seqlen = seqs[x]
+ * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) ) # <<<<<<<<<<<<<<
+ * bseqname = seqname.encode('ascii')
+ * strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_dest->target_name[__pyx_v_x]) = ((char *)calloc((__pyx_t_3 + 1), (sizeof(char))));
+
+ /* "csamtools.pyx":1397
+ * seqname, seqlen = seqs[x]
+ * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
+ * bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<<
+ * strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
+ * dest.target_len[x] = seqlen
+ */
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_seqname, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_114), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L10;
- }
- /*else*/ {
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!(likely(PyBytes_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(((PyObject *)__pyx_v_bseqname));
+ __pyx_v_bseqname = ((PyObject*)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1400
- * self.nextiter()
- * else:
- * raise StopIteration # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1398
+ * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
+ * bseqname = seqname.encode('ascii')
+ * strncpy( dest.target_name[x], bseqname, len(seqname) + 1 ) # <<<<<<<<<<<<<<
+ * dest.target_len[x] = seqlen
*
- * cdef class IteratorRowSelection(IteratorRow):
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_bseqname)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy((__pyx_v_dest->target_name[__pyx_v_x]), __pyx_t_13, (__pyx_t_3 + 1));
+
+ /* "csamtools.pyx":1399
+ * bseqname = seqname.encode('ascii')
+ * strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
+ * dest.target_len[x] = seqlen # <<<<<<<<<<<<<<
+ *
+ * return dest
+ */
+ __pyx_t_20 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_seqlen); if (unlikely((__pyx_t_20 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_dest->target_len[__pyx_v_x]) = __pyx_t_20;
}
- __pyx_L10:;
+ goto __pyx_L19;
}
+ __pyx_L19:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":1401
+ * dest.target_len[x] = seqlen
+ *
+ * return dest # <<<<<<<<<<<<<<
+ *
+ * ###############################################################
+ */
+ __pyx_r = __pyx_v_dest;
+ goto __pyx_L0;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__next__");
- __pyx_r = NULL;
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_XDECREF(__pyx_t_18);
+ __Pyx_WriteUnraisable("csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_XDECREF(__pyx_v_lines);
+ __Pyx_XDECREF(__pyx_v_record);
+ __Pyx_XDECREF(__pyx_v_ttype);
+ __Pyx_XDECREF(__pyx_v_data);
+ __Pyx_XDECREF(__pyx_v_fields);
+ __Pyx_XDECREF(__pyx_v_text);
+ __Pyx_XDECREF(__pyx_v_btext);
+ __Pyx_XDECREF(__pyx_v_bseqname);
+ __Pyx_XDECREF(__pyx_v_seqs);
+ __Pyx_XDECREF(__pyx_v_seqname);
+ __Pyx_XDECREF(__pyx_v_seqlen);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1415
- * cdef int owns_samfile
- *
- * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_40__iter__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1411
+ * ## Possible solutions: deprecate or open new file handle
+ * ###############################################################
+ * def __iter__(self): # <<<<<<<<<<<<<<
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam and self.samfile.header.n_targets == 0:
*/
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- PyObject *__pyx_v_positions = 0;
- int __pyx_v_reopen;
- PyObject *__pyx_v_mode;
- PyObject *__pyx_v_store;
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
int __pyx_t_4;
- char *__pyx_t_5;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
+ int __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1415);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[3] = {0,0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__positions);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
- if (value) { values[2] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- __pyx_v_positions = values[1];
- if (values[2]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else {
- __pyx_v_reopen = ((int)1);
- }
- } else {
- __pyx_v_reopen = ((int)1);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 3:
- __pyx_v_reopen = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 2)); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 2:
- __pyx_v_positions = PyTuple_GET_ITEM(__pyx_args, 1);
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
- break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_mode = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_store = Py_None; __Pyx_INCREF(Py_None);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1411);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1417
- * def __cinit__(self, Samfile samfile, positions, int reopen = True ):
- *
- * if not samfile._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
- *
+ /* "csamtools.pyx":1412
+ * ###############################################################
+ * def __iter__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam and self.samfile.header.n_targets == 0:
+ * raise NotImplementedError( "can not iterate over samfile without header")
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1418
- *
- * if not samfile._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_115), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1420
- * raise ValueError( "I/O operation on closed file" )
- *
- * if not samfile._isOpen(): # <<<<<<<<<<<<<<
- * raise ValueError( "I/O operation on closed file" )
- *
+ /* "csamtools.pyx":1413
+ * def __iter__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam and self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
+ * raise NotImplementedError( "can not iterate over samfile without header")
+ * return self
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = (!__pyx_t_4);
- if (__pyx_t_3) {
+ __pyx_t_4 = (!__pyx_v_self->isbam);
+ if (__pyx_t_4) {
+ __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_5 = __pyx_t_3;
+ } else {
+ __pyx_t_5 = __pyx_t_4;
+ }
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1421
- *
- * if not samfile._isOpen():
- * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1414
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam and self.samfile.header.n_targets == 0:
+ * raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<<
+ * return self
*
- * assert samfile.isbam, "can only use this iterator on bam files"
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1423
- * raise ValueError( "I/O operation on closed file" )
- *
- * assert samfile.isbam, "can only use this iterator on bam files" # <<<<<<<<<<<<<<
- * mode = "rb"
+ /* "csamtools.pyx":1415
+ * if not self.isbam and self.samfile.header.n_targets == 0:
+ * raise NotImplementedError( "can not iterate over samfile without header")
+ * return self # <<<<<<<<<<<<<<
*
+ * cdef bam1_t * getCurrent( self ):
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!__pyx_v_samfile->isbam)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_55));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.Samfile.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1424
+/* "csamtools.pyx":1417
+ * return self
*
- * assert samfile.isbam, "can only use this iterator on bam files"
- * mode = "rb" # <<<<<<<<<<<<<<
+ * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
+ * return self.b
*
- * # reopen the file to avoid iterator conflict
*/
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__rb);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1427
+static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ bam1_t *__pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1417);
+
+ /* "csamtools.pyx":1418
*
- * # reopen the file to avoid iterator conflict
- * if reopen: # <<<<<<<<<<<<<<
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
+ * cdef bam1_t * getCurrent( self ):
+ * return self.b # <<<<<<<<<<<<<<
+ *
+ * cdef int cnext(self):
*/
- if (__pyx_v_reopen) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1428
- * # reopen the file to avoid iterator conflict
- * if reopen:
- * store = StderrStore() # <<<<<<<<<<<<<<
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_store);
- __pyx_v_store = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1429
- * if reopen:
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
- * store.release()
- * assert self.fp != NULL
- */
- __pyx_t_5 = PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1430
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release() # <<<<<<<<<<<<<<
- * assert self.fp != NULL
- * self.owns_samfile = True
- */
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1431
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
- * assert self.fp != NULL # <<<<<<<<<<<<<<
- * self.owns_samfile = True
- * else:
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1432
- * store.release()
- * assert self.fp != NULL
- * self.owns_samfile = True # <<<<<<<<<<<<<<
- * else:
- * self.fp = samfile.samfile
- */
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L8;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1434
- * self.owns_samfile = True
- * else:
- * self.fp = samfile.samfile # <<<<<<<<<<<<<<
- * self.owns_samfile = False
- *
- */
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1435
- * else:
- * self.fp = samfile.samfile
- * self.owns_samfile = False # <<<<<<<<<<<<<<
- *
- * # allocate memory for alignment
- */
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 0;
- }
- __pyx_L8:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1438
- *
- * # allocate memory for alignment
- * self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
- *
- * self.positions = positions
- */
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1440
- * self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
- *
- * self.positions = positions # <<<<<<<<<<<<<<
- * self.current_pos = 0
- *
- */
- __Pyx_INCREF(__pyx_v_positions);
- __Pyx_GIVEREF(__pyx_v_positions);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
- __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions = __pyx_v_positions;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1441
- *
- * self.positions = positions
- * self.current_pos = 0 # <<<<<<<<<<<<<<
- *
- * def __iter__(self):
- */
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->current_pos = 0;
+ __pyx_r = __pyx_v_self->b;
+ goto __pyx_L0;
__pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__");
- __pyx_r = -1;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_mode);
- __Pyx_DECREF(__pyx_v_store);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1443
- * self.current_pos = 0
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
- *
- */
-
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection___iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1443);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1444
- *
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
- *
- * cdef bam1_t * getCurrent( self ):
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1446
- * return self
- *
- * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
+/* "csamtools.pyx":1420
* return self.b
*
+ * cdef int cnext(self): # <<<<<<<<<<<<<<
+ * '''
+ * cversion of iterator. Used by :class:`pysam.Samfile.IteratorColumn`.
*/
-static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
- bam1_t *__pyx_r;
+static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1446);
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1420);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1447
- *
- * cdef bam1_t * getCurrent( self ):
- * return self.b # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1425
+ * '''
+ * cdef int ret
+ * return samread(self.samfile, self.b) # <<<<<<<<<<<<<<
*
- * cdef int cnext(self):
+ * def __next__(self):
*/
- __pyx_r = __pyx_v_self->b;
+ __pyx_r = samread(__pyx_v_self->samfile, __pyx_v_self->b);
goto __pyx_L0;
__pyx_r = 0;
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1449
- * return self.b
- *
- * cdef int cnext(self): # <<<<<<<<<<<<<<
- * '''cversion of iterator'''
- *
- */
-
-static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
- int __pyx_r;
- Py_ssize_t __pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- uint64_t __pyx_t_4;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1449);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1453
- *
- * # end iteration if out of positions
- * if self.current_pos >= len(self.positions): return -1 # <<<<<<<<<<<<<<
- *
- * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
- */
- __pyx_t_1 = PyObject_Length(__pyx_v_self->positions); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = (__pyx_v_self->current_pos >= __pyx_t_1);
- if (__pyx_t_2) {
- __pyx_r = -1;
- goto __pyx_L0;
- goto __pyx_L3;
- }
- __pyx_L3:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1455
- * if self.current_pos >= len(self.positions): return -1
- *
- * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) # <<<<<<<<<<<<<<
- * self.current_pos += 1
- * return samread(self.fp, self.b)
- */
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_self->positions, __pyx_v_self->current_pos, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyInt_from_py_uint64_t(__pyx_t_3); if (unlikely((__pyx_t_4 == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- bam_seek(__pyx_v_self->fp->x.bam, __pyx_t_4, 0);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1456
- *
- * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
- * self.current_pos += 1 # <<<<<<<<<<<<<<
- * return samread(self.fp, self.b)
- *
- */
- __pyx_v_self->current_pos += 1;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1457
- * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
- * self.current_pos += 1
- * return samread(self.fp, self.b) # <<<<<<<<<<<<<<
- *
- * def __next__(self):
- */
- __pyx_r = samread(__pyx_v_self->fp, __pyx_v_self->b);
- goto __pyx_L0;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_WriteUnraisable("csamtools.IteratorRowSelection.cnext");
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_42__next__[] = "\n python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_42__next__;
+static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7Samfile_42__next__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1459
- * return samread(self.fp, self.b)
+/* "csamtools.pyx":1427
+ * return samread(self.samfile, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
- *
+ * """
+ * python version of next().
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_20IteratorRowSelection___next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__;
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection___next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1459);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1427);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1465
+ /* "csamtools.pyx":1432
* """
- *
- * cdef int ret = self.cnext() # <<<<<<<<<<<<<<
+ * cdef int ret
+ * ret = samread(self.samfile, self.b) # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __pyx_v_ret = samread(__pyx_v_self->samfile, __pyx_v_self->b);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1466
- *
- * cdef int ret = self.cnext()
+ /* "csamtools.pyx":1433
+ * cdef int ret
+ * ret = samread(self.samfile, self.b)
* if (ret > 0): # <<<<<<<<<<<<<<
* return makeAlignedRead( self.b )
* else:
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1467
- * cdef int ret = self.cnext()
+ /* "csamtools.pyx":1434
+ * ret = samread(self.samfile, self.b)
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
* else:
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1469
+ /* "csamtools.pyx":1436
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
*
- * def __dealloc__(self):
+ * ##-------------------------------------------------------------------
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowSelection.__next__");
+ __Pyx_AddTraceback("csamtools.Samfile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1471
- * raise StopIteration
- *
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * bam_destroy1(self.b)
- * if self.owns_samfile: samclose( self.fp )
- */
-
-static void __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(PyObject *__pyx_v_self) {
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1471);
+/* Python wrapper */
+static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ int __pyx_v_tid;
+ int __pyx_v_beg;
+ int __pyx_v_end;
+ int __pyx_v_reopen;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ {
+ PyObject* values[5] = {0,0,0,0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ case 2:
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg);
+ if (likely(values[2])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ case 3:
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[3])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ if (values[4]) {
+ } else {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1472
- *
- * def __dealloc__(self):
- * bam_destroy1(self.b) # <<<<<<<<<<<<<<
- * if self.owns_samfile: samclose( self.fp )
+ /* "csamtools.pyx":1481
+ * """
*
- */
- bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1473
- * def __dealloc__(self):
- * bam_destroy1(self.b)
- * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
+ * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
*
- * ##-------------------------------------------------------------------
+ * if not samfile._isOpen():
*/
- if (((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp);
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1486
- * int seq_len
- *
- * cdef int __advance_all( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
- * '''advance without any read filtering.
- * '''
- */
-
-static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_9csamtools___iterdata *__pyx_v_d;
- int __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_all");
- __Pyx_TraceCall("__advance_all", __pyx_f[0], 1486);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1490
- * '''
- * cdef __iterdata * d
- * d = <__iterdata*>data # <<<<<<<<<<<<<<
- * return bam_iter_read( d.samfile.x.bam, d.iter, b )
- *
- */
- __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1491
- * cdef __iterdata * d
- * d = <__iterdata*>data
- * return bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
- *
- * cdef int __advance_snpcalls( void * data, bam1_t * b ):
- */
- __pyx_r = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
+ __pyx_v_reopen = ((int)1);
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_beg = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_beg == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (values[4]) {
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_reopen = ((int)1);
+ }
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_beg, __pyx_v_end, __pyx_v_reopen);
goto __pyx_L0;
-
- __pyx_r = 0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1493
- * return bam_iter_read( d.samfile.x.bam, d.iter, b )
- *
- * cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
- * '''advance using same filter and read processing as in
- * the samtools pileup.
- */
-
-static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_9csamtools___iterdata *__pyx_v_d;
- int __pyx_v_ret;
- int __pyx_v_skip;
- int __pyx_v_q;
- int __pyx_v_is_cns;
- int __pyx_v_is_nobaq;
- int __pyx_v_capQ_thres;
+static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
- int __pyx_t_1;
- int __pyx_t_2;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- long __pyx_t_7;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_snpcalls");
- __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1493);
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1498
- * '''
- * cdef __iterdata * d
- * d = <__iterdata*>data # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1483
+ * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
+ *
+ * if not samfile._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
*
- * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*/
- __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1500
- * d = <__iterdata*>data
+ /* "csamtools.pyx":1484
*
- * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
- * cdef int skip = 0
- * cdef int q
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * if not samfile._hasIndex():
*/
- __pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_118), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1501
+ /* "csamtools.pyx":1486
+ * raise ValueError( "I/O operation on closed file" )
+ *
+ * if not samfile._hasIndex(): # <<<<<<<<<<<<<<
+ * raise ValueError( "no index available for iteration" )
*
- * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
- * cdef int skip = 0 # <<<<<<<<<<<<<<
- * cdef int q
- * cdef int is_cns = 1
*/
- __pyx_v_skip = 0;
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1503
- * cdef int skip = 0
- * cdef int q
- * cdef int is_cns = 1 # <<<<<<<<<<<<<<
- * cdef int is_nobaq = 0
- * cdef int capQ_thres = 0
+ /* "csamtools.pyx":1487
+ *
+ * if not samfile._hasIndex():
+ * raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
+ *
+ * # makes sure that samfile stays alive as long as the
*/
- __pyx_v_is_cns = 1;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_120), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1504
- * cdef int q
- * cdef int is_cns = 1
- * cdef int is_nobaq = 0 # <<<<<<<<<<<<<<
- * cdef int capQ_thres = 0
+ /* "csamtools.pyx":1491
+ * # makes sure that samfile stays alive as long as the
+ * # iterator is alive
+ * self.samfile = samfile # <<<<<<<<<<<<<<
*
+ * if samfile.isbam: mode = b"rb"
*/
- __pyx_v_is_nobaq = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1505
- * cdef int is_cns = 1
- * cdef int is_nobaq = 0
- * cdef int capQ_thres = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1493
+ * self.samfile = samfile
+ *
+ * if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
+ * else: mode = b"r"
*
- * # reload sequence
*/
- __pyx_v_capQ_thres = 0;
+ if (__pyx_v_samfile->isbam) {
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
+ __pyx_v_mode = __pyx_n_b__rb;
+ goto __pyx_L5;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1508
+ /* "csamtools.pyx":1494
*
- * # reload sequence
- * if d.fastafile != NULL and b.core.tid != d.tid: # <<<<<<<<<<<<<<
- * if d.seq != NULL: free(d.seq)
- * d.tid = b.core.tid
+ * if samfile.isbam: mode = b"rb"
+ * else: mode = b"r" # <<<<<<<<<<<<<<
+ *
+ * # reopen the file - note that this makes the iterator
*/
- __pyx_t_1 = (__pyx_v_d->fastafile != NULL);
- if (__pyx_t_1) {
- __pyx_t_2 = (__pyx_v_b->core.tid != __pyx_v_d->tid);
- __pyx_t_3 = __pyx_t_2;
- } else {
- __pyx_t_3 = __pyx_t_1;
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__r));
+ __pyx_v_mode = __pyx_n_b__r;
}
- if (__pyx_t_3) {
+ __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1509
- * # reload sequence
- * if d.fastafile != NULL and b.core.tid != d.tid:
- * if d.seq != NULL: free(d.seq) # <<<<<<<<<<<<<<
- * d.tid = b.core.tid
- * d.seq = faidx_fetch_seq(d.fastafile,
+ /* "csamtools.pyx":1498
+ * # reopen the file - note that this makes the iterator
+ * # slow and causes pileup to slow down significantly.
+ * if reopen: # <<<<<<<<<<<<<<
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
*/
- __pyx_t_3 = (__pyx_v_d->seq != NULL);
- if (__pyx_t_3) {
- free(__pyx_v_d->seq);
- goto __pyx_L4;
- }
- __pyx_L4:;
+ if (__pyx_v_reopen) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1510
- * if d.fastafile != NULL and b.core.tid != d.tid:
- * if d.seq != NULL: free(d.seq)
- * d.tid = b.core.tid # <<<<<<<<<<<<<<
- * d.seq = faidx_fetch_seq(d.fastafile,
- * d.samfile.header.target_name[d.tid],
+ /* "csamtools.pyx":1499
+ * # slow and causes pileup to slow down significantly.
+ * if reopen:
+ * store = StderrStore() # <<<<<<<<<<<<<<
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
*/
- __pyx_v_d->tid = __pyx_v_b->core.tid;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_store = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1511
- * if d.seq != NULL: free(d.seq)
- * d.tid = b.core.tid
- * d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<<
- * d.samfile.header.target_name[d.tid],
- * 0, max_pos,
+ /* "csamtools.pyx":1500
+ * if reopen:
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
+ * store.release()
+ * assert self.fp != NULL
*/
- __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_9csamtools_max_pos, (&__pyx_v_d->seq_len));
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1515
- * 0, max_pos,
- * &d.seq_len)
- * if d.seq == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
- * (d.samfile.header.target_name[d.tid],
+ /* "csamtools.pyx":1501
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release() # <<<<<<<<<<<<<<
+ * assert self.fp != NULL
+ * self.owns_samfile = True
*/
- __pyx_t_3 = (__pyx_v_d->seq == NULL);
- if (__pyx_t_3) {
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1517
- * if d.seq == NULL:
- * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
- * (d.samfile.header.target_name[d.tid], # <<<<<<<<<<<<<<
- * d.tid))
- *
+ /* "csamtools.pyx":1502
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ * assert self.fp != NULL # <<<<<<<<<<<<<<
+ * self.owns_samfile = True
+ * else:
*/
- __pyx_t_4 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ PyErr_SetNone(PyExc_AssertionError);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1518
- * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
- * (d.samfile.header.target_name[d.tid],
- * d.tid)) # <<<<<<<<<<<<<<
- *
- *
+ /* "csamtools.pyx":1503
+ * store.release()
+ * assert self.fp != NULL
+ * self.owns_samfile = True # <<<<<<<<<<<<<<
+ * else:
+ * self.fp = self.samfile.samfile
*/
- __pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_4 = 0;
- __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_56), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
- goto __pyx_L3;
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1521
- *
- *
- * while ret >= 0: # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1505
+ * self.owns_samfile = True
+ * else:
+ * self.fp = self.samfile.samfile # <<<<<<<<<<<<<<
+ * self.owns_samfile = False
*
- * skip = 0
*/
- while (1) {
- __pyx_t_3 = (__pyx_v_ret >= 0);
- if (!__pyx_t_3) break;
+ __pyx_v_self->fp = __pyx_v_self->samfile->samfile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1523
- * while ret >= 0:
- *
- * skip = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1506
+ * else:
+ * self.fp = self.samfile.samfile
+ * self.owns_samfile = False # <<<<<<<<<<<<<<
*
- * # realign read - changes base qualities
+ * self.retval = 0
*/
- __pyx_v_skip = 0;
+ __pyx_v_self->owns_samfile = 0;
+ }
+ __pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1526
+ /* "csamtools.pyx":1508
+ * self.owns_samfile = False
*
- * # realign read - changes base qualities
- * if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq ) # <<<<<<<<<<<<<<
+ * self.retval = 0 # <<<<<<<<<<<<<<
*
- * if d.seq != NULL and capQ_thres > 10:
+ * self.iter = bam_iter_query(self.samfile.index,
*/
- __pyx_t_3 = (__pyx_v_d->seq != NULL);
- if (__pyx_t_3) {
- if (__pyx_v_is_cns) {
- __pyx_t_1 = (!__pyx_v_is_nobaq);
- __pyx_t_2 = __pyx_t_1;
- } else {
- __pyx_t_2 = __pyx_v_is_cns;
- }
- __pyx_t_1 = __pyx_t_2;
- } else {
- __pyx_t_1 = __pyx_t_3;
- }
- if (__pyx_t_1) {
- bam_prob_realn(__pyx_v_b, __pyx_v_d->seq);
- goto __pyx_L8;
- }
- __pyx_L8:;
+ __pyx_v_self->retval = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1528
- * if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq )
+ /* "csamtools.pyx":1510
+ * self.retval = 0
*
- * if d.seq != NULL and capQ_thres > 10: # <<<<<<<<<<<<<<
- * q = bam_cap_mapQ(b, d.seq, capQ_thres)
- * if q < 0: skip = 1
+ * self.iter = bam_iter_query(self.samfile.index, # <<<<<<<<<<<<<<
+ * tid,
+ * beg,
*/
- __pyx_t_1 = (__pyx_v_d->seq != NULL);
- if (__pyx_t_1) {
- __pyx_t_3 = (__pyx_v_capQ_thres > 10);
- __pyx_t_2 = __pyx_t_3;
- } else {
- __pyx_t_2 = __pyx_t_1;
- }
- if (__pyx_t_2) {
+ __pyx_v_self->iter = bam_iter_query(__pyx_v_self->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1529
+ /* "csamtools.pyx":1514
+ * beg,
+ * end)
+ * self.b = bam_init1() # <<<<<<<<<<<<<<
*
- * if d.seq != NULL and capQ_thres > 10:
- * q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
- * if q < 0: skip = 1
- * elif b.core.qual > q: b.core.qual = q
+ * def __iter__(self):
*/
- __pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
+ __pyx_v_self->b = bam_init1();
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1530
- * if d.seq != NULL and capQ_thres > 10:
- * q = bam_cap_mapQ(b, d.seq, capQ_thres)
- * if q < 0: skip = 1 # <<<<<<<<<<<<<<
- * elif b.core.qual > q: b.core.qual = q
- * if b.core.flag & BAM_FUNMAP: skip = 1
- */
- __pyx_t_2 = (__pyx_v_q < 0);
- if (__pyx_t_2) {
- __pyx_v_skip = 1;
- goto __pyx_L10;
- }
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_mode);
+ __Pyx_XDECREF(__pyx_v_store);
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1531
- * q = bam_cap_mapQ(b, d.seq, capQ_thres)
- * if q < 0: skip = 1
- * elif b.core.qual > q: b.core.qual = q # <<<<<<<<<<<<<<
- * if b.core.flag & BAM_FUNMAP: skip = 1
- * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
- */
- __pyx_t_2 = (__pyx_v_b->core.qual > __pyx_v_q);
- if (__pyx_t_2) {
- __pyx_v_b->core.qual = __pyx_v_q;
- goto __pyx_L10;
- }
- __pyx_L10:;
- goto __pyx_L9;
- }
- __pyx_L9:;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1532
- * if q < 0: skip = 1
- * elif b.core.qual > q: b.core.qual = q
- * if b.core.flag & BAM_FUNMAP: skip = 1 # <<<<<<<<<<<<<<
- * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
+/* "csamtools.pyx":1516
+ * self.b = bam_init1()
*
- */
- __pyx_t_7 = (__pyx_v_b->core.flag & 4);
- if (__pyx_t_7) {
- __pyx_v_skip = 1;
- goto __pyx_L11;
- }
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1533
- * elif b.core.qual > q: b.core.qual = q
- * if b.core.flag & BAM_FUNMAP: skip = 1
- * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 # <<<<<<<<<<<<<<
+ * def __iter__(self): # <<<<<<<<<<<<<<
+ * return self
*
- * if not skip: break
*/
- if ((__pyx_v_b->core.flag & 1)) {
- __pyx_t_2 = (!(__pyx_v_b->core.flag & 2));
- __pyx_t_1 = __pyx_t_2;
- } else {
- __pyx_t_1 = (__pyx_v_b->core.flag & 1);
- }
- if (__pyx_t_1) {
- __pyx_v_skip = 1;
- goto __pyx_L11;
- }
- __pyx_L11:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1535
- * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1516);
+
+ /* "csamtools.pyx":1517
*
- * if not skip: break # <<<<<<<<<<<<<<
- * # additional filters
+ * def __iter__(self):
+ * return self # <<<<<<<<<<<<<<
*
+ * cdef bam1_t * getCurrent( self ):
*/
- __pyx_t_1 = (!__pyx_v_skip);
- if (__pyx_t_1) {
- goto __pyx_L7_break;
- goto __pyx_L12;
- }
- __pyx_L12:;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1538
- * # additional filters
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1519
+ * return self
*
- * ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
+ * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
+ * return self.b
*
- * return ret
*/
- __pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
- }
- __pyx_L7_break:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1540
- * ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
+static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+ bam1_t *__pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1519);
+
+ /* "csamtools.pyx":1520
*
- * return ret # <<<<<<<<<<<<<<
+ * cdef bam1_t * getCurrent( self ):
+ * return self.b # <<<<<<<<<<<<<<
*
- * cdef class IteratorColumn:
+ * cdef int cnext(self):
*/
- __pyx_r = __pyx_v_ret;
+ __pyx_r = __pyx_v_self->b;
goto __pyx_L0;
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_WriteUnraisable("csamtools.__advance_snpcalls");
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1599
- * cdef stepper
+/* "csamtools.pyx":1522
+ * return self.b
*
- * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ * cdef int cnext(self): # <<<<<<<<<<<<<<
+ * '''cversion of iterator. Used by IteratorColumn'''
+ * self.retval = bam_iter_read( self.fp.x.bam,
*/
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- PyObject *__pyx_v_kwargs = 0;
+static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1599);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1522);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1600
- *
- * def __cinit__( self, Samfile samfile, **kwargs ):
- * self.samfile = samfile # <<<<<<<<<<<<<<
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
- * self.fastafile = kwargs.get( "fastafile", None )
+ /* "csamtools.pyx":1524
+ * cdef int cnext(self):
+ * '''cversion of iterator. Used by IteratorColumn'''
+ * self.retval = bam_iter_read( self.fp.x.bam, # <<<<<<<<<<<<<<
+ * self.iter,
+ * self.b)
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile = __pyx_v_samfile;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1601
- * def __cinit__( self, Samfile samfile, **kwargs ):
- * self.samfile = samfile
- * self.mask = kwargs.get("mask", BAM_DEF_MASK ) # <<<<<<<<<<<<<<
- * self.fastafile = kwargs.get( "fastafile", None )
- * self.stepper = kwargs.get( "stepper", None )
- */
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__mask), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->mask = __pyx_t_3;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1602
- * self.samfile = samfile
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
- * self.fastafile = kwargs.get( "fastafile", None ) # <<<<<<<<<<<<<<
- * self.stepper = kwargs.get( "stepper", None )
- * self.iterdata.seq = NULL
- */
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__fastafile), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_t_2);
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1603
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
- * self.fastafile = kwargs.get( "fastafile", None )
- * self.stepper = kwargs.get( "stepper", None ) # <<<<<<<<<<<<<<
- * self.iterdata.seq = NULL
- * self.tid = 0
- */
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__stepper), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
- __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1604
- * self.fastafile = kwargs.get( "fastafile", None )
- * self.stepper = kwargs.get( "stepper", None )
- * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
- * self.tid = 0
- * self.pos = 0
- */
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1605
- * self.stepper = kwargs.get( "stepper", None )
- * self.iterdata.seq = NULL
- * self.tid = 0 # <<<<<<<<<<<<<<
- * self.pos = 0
- * self.n_plp = 0
- */
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->tid = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1606
- * self.iterdata.seq = NULL
- * self.tid = 0
- * self.pos = 0 # <<<<<<<<<<<<<<
- * self.n_plp = 0
- * self.plp = NULL
- */
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pos = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1607
- * self.tid = 0
- * self.pos = 0
- * self.n_plp = 0 # <<<<<<<<<<<<<<
- * self.plp = NULL
- * self.pileup_iter = <bam_plp_t>NULL
- */
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->n_plp = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1608
- * self.pos = 0
- * self.n_plp = 0
- * self.plp = NULL # <<<<<<<<<<<<<<
- * self.pileup_iter = <bam_plp_t>NULL
- *
- */
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->plp = NULL;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1609
- * self.n_plp = 0
- * self.plp = NULL
- * self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
- *
- * def __iter__(self):
- */
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
+ __pyx_v_self->retval = bam_iter_read(__pyx_v_self->fp->x.bam, __pyx_v_self->iter, __pyx_v_self->b);
__pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1611
- * self.pileup_iter = <bam_plp_t>NULL
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_17IteratorRowRegion_4__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__;
+static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion_4__next__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1528
+ * self.b)
*
+ * def __next__(self): # <<<<<<<<<<<<<<
+ * """python version of next().
+ * """
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn___iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1611);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1528);
+
+ /* "csamtools.pyx":1531
+ * """python version of next().
+ * """
+ * self.cnext() # <<<<<<<<<<<<<<
+ * if self.retval < 0: raise StopIteration
+ * return makeAlignedRead( self.b )
+ */
+ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1612
+ /* "csamtools.pyx":1532
+ * """
+ * self.cnext()
+ * if self.retval < 0: raise StopIteration # <<<<<<<<<<<<<<
+ * return makeAlignedRead( self.b )
*
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
+ */
+ __pyx_t_1 = (__pyx_v_self->retval < 0);
+ if (__pyx_t_1) {
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":1533
+ * self.cnext()
+ * if self.retval < 0: raise StopIteration
+ * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
*
- * cdef int cnext(self):
+ * def __dealloc__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorRowRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1614
- * return self
- *
- * cdef int cnext(self): # <<<<<<<<<<<<<<
- * '''perform next iteration.
+/* Python wrapper */
+static void __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "csamtools.pyx":1535
+ * return makeAlignedRead( self.b )
*
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * bam_destroy1(self.b)
+ * bam_iter_destroy( self.iter )
*/
-static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
- int __pyx_r;
+static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1614);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1535);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1620
- * It has been re-implemented to permit for filtering.
- * '''
- * self.plp = bam_plp_auto( self.pileup_iter, # <<<<<<<<<<<<<<
- * &self.tid,
- * &self.pos,
+ /* "csamtools.pyx":1536
+ *
+ * def __dealloc__(self):
+ * bam_destroy1(self.b) # <<<<<<<<<<<<<<
+ * bam_iter_destroy( self.iter )
+ * if self.owns_samfile: samclose( self.fp )
*/
- __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
-
- __pyx_r = 0;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ bam_destroy1(__pyx_v_self->b);
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1625
- * &self.n_plp )
+ /* "csamtools.pyx":1537
+ * def __dealloc__(self):
+ * bam_destroy1(self.b)
+ * bam_iter_destroy( self.iter ) # <<<<<<<<<<<<<<
+ * if self.owns_samfile: samclose( self.fp )
*
- * cdef char * getSequence( self ): # <<<<<<<<<<<<<<
- * '''return current reference sequence underlying the iterator.
- * '''
*/
+ bam_iter_destroy(__pyx_v_self->iter);
-static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
- char *__pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getSequence");
- __Pyx_TraceCall("getSequence", __pyx_f[0], 1625);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1628
- * '''return current reference sequence underlying the iterator.
- * '''
- * return self.iterdata.seq # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1538
+ * bam_destroy1(self.b)
+ * bam_iter_destroy( self.iter )
+ * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
- * property seq_len:
+ * cdef class IteratorRowAll(IteratorRow):
*/
- __pyx_r = __pyx_v_self->iterdata.seq;
- goto __pyx_L0;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- __pyx_r = 0;
- __pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
- return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1632
- * property seq_len:
- * '''current sequence length.'''
- * def __get__(self): return self.iterdata.seq_len # <<<<<<<<<<<<<<
+/* Python wrapper */
+static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ int __pyx_v_reopen;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ {
+ PyObject* values[2] = {0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ if (values[1]) {
+ } else {
+
+ /* "csamtools.pyx":1550
+ * """
*
- * def addReference( self, Fastafile fastafile ):
+ * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
*/
-
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1632);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_v_reopen = ((int)1);
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ if (values[1]) {
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_reopen = ((int)1);
+ }
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_14IteratorRowAll___cinit__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IteratorColumn.seq_len.__get__");
- __pyx_r = NULL;
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1634
- * def __get__(self): return self.iterdata.seq_len
- *
- * def addReference( self, Fastafile fastafile ): # <<<<<<<<<<<<<<
- * '''
- * add reference sequences in *fastafile* to iterator.'''
- */
-
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorColumn_addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
+static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("addReference");
- __Pyx_TraceCall("addReference", __pyx_f[0], 1634);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1550);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1637
- * '''
- * add reference sequences in *fastafile* to iterator.'''
- * self.fastafile = fastafile # <<<<<<<<<<<<<<
- * if self.iterdata.seq != NULL: free(self.iterdata.seq)
- * self.iterdata.tid = -1
+ /* "csamtools.pyx":1552
+ * def __cinit__(self, Samfile samfile, int reopen = True ):
+ *
+ * if not samfile._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
+ *
*/
- __Pyx_INCREF(__pyx_v_fastafile);
- __Pyx_GIVEREF(__pyx_v_fastafile);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_fastafile);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1638
- * add reference sequences in *fastafile* to iterator.'''
- * self.fastafile = fastafile
- * if self.iterdata.seq != NULL: free(self.iterdata.seq) # <<<<<<<<<<<<<<
- * self.iterdata.tid = -1
- * self.iterdata.fastafile = self.fastafile.fastafile
+ /* "csamtools.pyx":1553
+ *
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * if samfile.isbam: mode = b"rb"
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
- if (__pyx_t_1) {
- free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_121), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":1555
+ * raise ValueError( "I/O operation on closed file" )
+ *
+ * if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
+ * else: mode = b"r"
+ *
+ */
+ if (__pyx_v_samfile->isbam) {
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
+ __pyx_v_mode = __pyx_n_b__rb;
+ goto __pyx_L4;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":1556
+ *
+ * if samfile.isbam: mode = b"rb"
+ * else: mode = b"r" # <<<<<<<<<<<<<<
+ *
+ * # reopen the file to avoid iterator conflict
+ */
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__r));
+ __pyx_v_mode = __pyx_n_b__r;
+ }
+ __pyx_L4:;
+
+ /* "csamtools.pyx":1559
+ *
+ * # reopen the file to avoid iterator conflict
+ * if reopen: # <<<<<<<<<<<<<<
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ */
+ if (__pyx_v_reopen) {
+
+ /* "csamtools.pyx":1560
+ * # reopen the file to avoid iterator conflict
+ * if reopen:
+ * store = StderrStore() # <<<<<<<<<<<<<<
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ */
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_store = __pyx_t_1;
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":1561
+ * if reopen:
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
+ * store.release()
+ * assert self.fp != NULL
+ */
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+
+ /* "csamtools.pyx":1562
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release() # <<<<<<<<<<<<<<
+ * assert self.fp != NULL
+ * self.owns_samfile = True
+ */
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":1563
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ * assert self.fp != NULL # <<<<<<<<<<<<<<
+ * self.owns_samfile = True
+ * else:
+ */
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ PyErr_SetNone(PyExc_AssertionError);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
+
+ /* "csamtools.pyx":1564
+ * store.release()
+ * assert self.fp != NULL
+ * self.owns_samfile = True # <<<<<<<<<<<<<<
+ * else:
+ * self.fp = samfile.samfile
+ */
+ __pyx_v_self->owns_samfile = 1;
goto __pyx_L5;
}
- __pyx_L5:;
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1639
- * self.fastafile = fastafile
- * if self.iterdata.seq != NULL: free(self.iterdata.seq)
- * self.iterdata.tid = -1 # <<<<<<<<<<<<<<
- * self.iterdata.fastafile = self.fastafile.fastafile
+ /* "csamtools.pyx":1566
+ * self.owns_samfile = True
+ * else:
+ * self.fp = samfile.samfile # <<<<<<<<<<<<<<
+ * self.owns_samfile = False
*
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.tid = -1;
+ __pyx_v_self->fp = __pyx_v_samfile->samfile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1640
- * if self.iterdata.seq != NULL: free(self.iterdata.seq)
- * self.iterdata.tid = -1
- * self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1567
+ * else:
+ * self.fp = samfile.samfile
+ * self.owns_samfile = False # <<<<<<<<<<<<<<
*
- * def hasReference( self ):
+ * # allocate memory for alignment
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.fastafile = ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile->fastafile;
+ __pyx_v_self->owns_samfile = 0;
+ }
+ __pyx_L5:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":1570
+ *
+ * # allocate memory for alignment
+ * self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
+ *
+ * def __iter__(self):
+ */
+ __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.IteratorColumn.addReference");
- __pyx_r = NULL;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_XDECREF(__pyx_v_mode);
+ __Pyx_XDECREF(__pyx_v_store);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1642
- * self.iterdata.fastafile = self.fastafile.fastafile
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_14IteratorRowAll_2__iter__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1572
+ * self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
+ *
+ * def __iter__(self): # <<<<<<<<<<<<<<
+ * return self
*
- * def hasReference( self ): # <<<<<<<<<<<<<<
- * '''
- * return true if iterator is associated with a reference'''
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorColumn_hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("hasReference");
- __Pyx_TraceCall("hasReference", __pyx_f[0], 1642);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1572);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1645
- * '''
- * return true if iterator is associated with a reference'''
- * return self.fastafile # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1573
*
- * cdef setMask( self, mask ):
+ * def __iter__(self):
+ * return self # <<<<<<<<<<<<<<
+ *
+ * cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
- __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1647
- * return self.fastafile
+/* "csamtools.pyx":1575
+ * return self
*
- * cdef setMask( self, mask ): # <<<<<<<<<<<<<<
- * '''set masking flag in iterator.
+ * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
+ * return self.b
*
*/
-static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_mask) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
+static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+ bam1_t *__pyx_r;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setMask");
- __Pyx_TraceCall("setMask", __pyx_f[0], 1647);
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1575);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1652
- * reads with bits set in *mask* will be skipped.
- * '''
- * self.mask = mask # <<<<<<<<<<<<<<
- * bam_plp_set_mask( self.pileup_iter, self.mask )
+ /* "csamtools.pyx":1576
+ *
+ * cdef bam1_t * getCurrent( self ):
+ * return self.b # <<<<<<<<<<<<<<
*
+ * cdef int cnext(self):
*/
- __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_mask); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->mask = __pyx_t_1;
+ __pyx_r = __pyx_v_self->b;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1653
- * '''
- * self.mask = mask
- * bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1578
+ * return self.b
*
- * cdef setupIteratorData( self,
+ * cdef int cnext(self): # <<<<<<<<<<<<<<
+ * '''cversion of iterator. Used by IteratorColumn'''
+ * return samread(self.fp, self.b)
*/
- bam_plp_set_mask(__pyx_v_self->pileup_iter, __pyx_v_self->mask);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1578);
+
+ /* "csamtools.pyx":1580
+ * cdef int cnext(self):
+ * '''cversion of iterator. Used by IteratorColumn'''
+ * return samread(self.fp, self.b) # <<<<<<<<<<<<<<
+ *
+ * def __next__(self):
+ */
+ __pyx_r = samread(__pyx_v_self->fp, __pyx_v_self->b);
goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.IteratorColumn.setMask");
+
__pyx_r = 0;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1655
- * bam_plp_set_mask( self.pileup_iter, self.mask )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorRowAll_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__;
+static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_14IteratorRowAll_4__next__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1582
+ * return samread(self.fp, self.b)
+ *
+ * def __next__(self): # <<<<<<<<<<<<<<
+ * """python version of next().
*
- * cdef setupIteratorData( self, # <<<<<<<<<<<<<<
- * int tid,
- * int start,
*/
-static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args) {
- int __pyx_v_reopen = ((int)0);
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+ int __pyx_v_ret;
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- int __pyx_t_6;
- int __pyx_t_7;
- int __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setupIteratorData");
- __Pyx_TraceCall("setupIteratorData", __pyx_f[0], 1655);
- if (__pyx_optional_args) {
- if (__pyx_optional_args->__pyx_n > 0) {
- __pyx_v_reopen = __pyx_optional_args->reopen;
- }
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1582);
+
+ /* "csamtools.pyx":1588
+ * """
+ * cdef int ret
+ * ret = samread(self.fp, self.b) # <<<<<<<<<<<<<<
+ * if (ret > 0):
+ * return makeAlignedRead( self.b )
+ */
+ __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_self->b);
+
+ /* "csamtools.pyx":1589
+ * cdef int ret
+ * ret = samread(self.fp, self.b)
+ * if (ret > 0): # <<<<<<<<<<<<<<
+ * return makeAlignedRead( self.b )
+ * else:
+ */
+ __pyx_t_1 = (__pyx_v_ret > 0);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":1590
+ * ret = samread(self.fp, self.b)
+ * if (ret > 0):
+ * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
+ * else:
+ * raise StopIteration
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
}
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1662
- * '''setup the iterator structure'''
+ /* "csamtools.pyx":1592
+ * return makeAlignedRead( self.b )
+ * else:
+ * raise StopIteration # <<<<<<<<<<<<<<
*
- * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen ) # <<<<<<<<<<<<<<
- * self.iterdata.samfile = self.samfile.samfile
- * self.iterdata.iter = self.iter.iter
+ * def __dealloc__(self):
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyInt_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_self->samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_1 = 0;
- __pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), __pyx_t_5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_GIVEREF(__pyx_t_4);
- __Pyx_GOTREF(__pyx_v_self->iter);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
- __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_4);
- __pyx_t_4 = 0;
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1663
- *
- * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
- * self.iterdata.samfile = self.samfile.samfile # <<<<<<<<<<<<<<
- * self.iterdata.iter = self.iter.iter
- * self.iterdata.seq = NULL
- */
- __pyx_v_self->iterdata.samfile = __pyx_v_self->samfile->samfile;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorRowAll.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1664
- * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
- * self.iterdata.samfile = self.samfile.samfile
- * self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
- * self.iterdata.seq = NULL
- * self.iterdata.tid = -1
- */
- __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
+/* Python wrapper */
+static void __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1665
- * self.iterdata.samfile = self.samfile.samfile
- * self.iterdata.iter = self.iter.iter
- * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
- * self.iterdata.tid = -1
+/* "csamtools.pyx":1594
+ * raise StopIteration
*
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * bam_destroy1(self.b)
+ * if self.owns_samfile: samclose( self.fp )
*/
- __pyx_v_self->iterdata.seq = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1666
- * self.iterdata.iter = self.iter.iter
- * self.iterdata.seq = NULL
- * self.iterdata.tid = -1 # <<<<<<<<<<<<<<
- *
- * if self.fastafile != None:
- */
- __pyx_v_self->iterdata.tid = -1;
+static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1594);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1668
- * self.iterdata.tid = -1
+ /* "csamtools.pyx":1595
+ *
+ * def __dealloc__(self):
+ * bam_destroy1(self.b) # <<<<<<<<<<<<<<
+ * if self.owns_samfile: samclose( self.fp )
*
- * if self.fastafile != None: # <<<<<<<<<<<<<<
- * self.iterdata.fastafile = self.fastafile.fastafile
- * else:
*/
- __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_self->fastafile), Py_None, Py_NE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_6) {
+ bam_destroy1(__pyx_v_self->b);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1669
+ /* "csamtools.pyx":1596
+ * def __dealloc__(self):
+ * bam_destroy1(self.b)
+ * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
- * if self.fastafile != None:
- * self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
- * else:
- * self.iterdata.fastafile = NULL
+ * cdef class IteratorRowAllRefs(IteratorRow):
*/
- __pyx_v_self->iterdata.fastafile = __pyx_v_self->fastafile->fastafile;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
goto __pyx_L3;
}
- /*else*/ {
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1671
- * self.iterdata.fastafile = self.fastafile.fastafile
- * else:
- * self.iterdata.fastafile = NULL # <<<<<<<<<<<<<<
- *
- * if self.stepper == None or self.stepper == "all":
- */
- __pyx_v_self->iterdata.fastafile = NULL;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+}
+
+/* Python wrapper */
+static int __pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ {
+ PyObject* values[1] = {0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ }
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
}
- __pyx_L3:;
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self), __pyx_v_samfile);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1673
- * self.iterdata.fastafile = NULL
+/* "csamtools.pyx":1602
+ * """
*
- * if self.stepper == None or self.stepper == "all": # <<<<<<<<<<<<<<
- * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
- * elif self.stepper == "samtools":
+ * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, Py_None, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!__pyx_t_6) {
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_8 = __pyx_t_7;
- } else {
- __pyx_t_8 = __pyx_t_6;
- }
- if (__pyx_t_8) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1674
+static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1602);
+
+ /* "csamtools.pyx":1603
*
- * if self.stepper == None or self.stepper == "all":
- * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata ) # <<<<<<<<<<<<<<
- * elif self.stepper == "samtools":
- * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
+ * def __cinit__(self, Samfile samfile):
+ * assert samfile._isOpen() # <<<<<<<<<<<<<<
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ * self.samfile = samfile
*/
- __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_all), (&__pyx_v_self->iterdata));
- goto __pyx_L4;
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (unlikely(!__pyx_t_3)) {
+ PyErr_SetNone(PyExc_AssertionError);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1675
- * if self.stepper == None or self.stepper == "all":
- * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
- * elif self.stepper == "samtools": # <<<<<<<<<<<<<<
- * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
- * else:
- */
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__samtools), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_8) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1676
- * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
- * elif self.stepper == "samtools":
- * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata ) # <<<<<<<<<<<<<<
- * else:
- * raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
+ /* "csamtools.pyx":1604
+ * def __cinit__(self, Samfile samfile):
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ * self.tid = -1
*/
- __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_snpcalls), (&__pyx_v_self->iterdata));
- goto __pyx_L4;
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- /*else*/ {
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1678
- * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
- * else:
- * raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1605
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ * self.samfile = samfile # <<<<<<<<<<<<<<
+ * self.tid = -1
*
- * bam_plp_set_mask( self.pileup_iter, self.mask )
*/
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_57), __pyx_v_self->stepper); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L4:;
+ __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1680
- * raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
- *
- * bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1606
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ * self.samfile = samfile
+ * self.tid = -1 # <<<<<<<<<<<<<<
*
- * cdef reset( self, tid, start, end ):
+ * def nextiter(self):
*/
- bam_plp_set_mask(__pyx_v_self->pileup_iter, __pyx_v_self->mask);
+ __pyx_v_self->tid = -1;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IteratorColumn.setupIteratorData");
- __pyx_r = 0;
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1682
- * bam_plp_set_mask( self.pileup_iter, self.mask )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_18IteratorRowAllRefs_2nextiter[] = "IteratorRowAllRefs.nextiter(self)";
+static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("nextiter (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1608
+ * self.tid = -1
*
- * cdef reset( self, tid, start, end ): # <<<<<<<<<<<<<<
- * '''reset iterator position.
+ * def nextiter(self): # <<<<<<<<<<<<<<
+ * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
*
*/
-static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_end) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset");
- __Pyx_TraceCall("reset", __pyx_f[0], 1682);
+ __Pyx_RefNannySetupContext("nextiter", 0);
+ __Pyx_TraceCall("nextiter", __pyx_f[0], 1608);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1688
- * having to incur the full set-up costs.
- * '''
- * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 ) # <<<<<<<<<<<<<<
- * self.iterdata.iter = self.iter.iter
+ /* "csamtools.pyx":1609
+ *
+ * def nextiter(self):
+ * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29) # <<<<<<<<<<<<<<
*
+ * def __iter__(self):
*/
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
- __Pyx_INCREF(__pyx_v_tid);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_tid);
- __Pyx_GIVEREF(__pyx_v_tid);
- __Pyx_INCREF(__pyx_v_start);
- PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_start);
- __Pyx_GIVEREF(__pyx_v_start);
- __Pyx_INCREF(__pyx_v_end);
- PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_end);
- __Pyx_GIVEREF(__pyx_v_end);
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), __pyx_t_1, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
+ __Pyx_INCREF(__pyx_int_536870912);
+ PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_int_536870912);
+ __Pyx_GIVEREF(__pyx_int_536870912);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_GIVEREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_v_self->iter);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
- __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_3);
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1689
- * '''
- * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 )
- * self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
- *
- * # invalidate sequence if different tid
- */
- __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_v_self->rowiter);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->rowiter));
+ __pyx_v_self->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1692
- *
- * # invalidate sequence if different tid
- * if self.tid != tid: # <<<<<<<<<<<<<<
- * if self.iterdata.seq != NULL: free( self.iterdata.seq )
- * self.iterdata.seq = NULL
- */
- __pyx_t_3 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_v_tid, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_4) {
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.nextiter", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1693
- * # invalidate sequence if different tid
- * if self.tid != tid:
- * if self.iterdata.seq != NULL: free( self.iterdata.seq ) # <<<<<<<<<<<<<<
- * self.iterdata.seq = NULL
- * self.iterdata.tid = -1
- */
- __pyx_t_4 = (__pyx_v_self->iterdata.seq != NULL);
- if (__pyx_t_4) {
- free(__pyx_v_self->iterdata.seq);
- goto __pyx_L4;
- }
- __pyx_L4:;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1694
- * if self.tid != tid:
- * if self.iterdata.seq != NULL: free( self.iterdata.seq )
- * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
- * self.iterdata.tid = -1
+/* "csamtools.pyx":1611
+ * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
*
- */
- __pyx_v_self->iterdata.seq = NULL;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1695
- * if self.iterdata.seq != NULL: free( self.iterdata.seq )
- * self.iterdata.seq = NULL
- * self.iterdata.tid = -1 # <<<<<<<<<<<<<<
+ * def __iter__(self): # <<<<<<<<<<<<<<
+ * return self
*
- * # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata )
*/
- __pyx_v_self->iterdata.tid = -1;
- goto __pyx_L3;
- }
- __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1698
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1611);
+
+ /* "csamtools.pyx":1612
*
- * # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata )
- * bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
+ * def __iter__(self):
+ * return self # <<<<<<<<<<<<<<
*
- * def __dealloc__(self):
+ * def __next__(self):
*/
- bam_plp_reset(__pyx_v_self->pileup_iter);
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IteratorColumn.reset");
- __pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1700
- * bam_plp_reset(self.pileup_iter)
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__;
+static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1614
+ * return self
+ *
+ * def __next__(self): # <<<<<<<<<<<<<<
+ * """python version of next().
*
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * # reset in order to avoid memory leak messages for iterators that have
- * # not been fully consumed
*/
-static void __pyx_pf_9csamtools_14IteratorColumn___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_14IteratorColumn___dealloc__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1700);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1614);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1703
- * # reset in order to avoid memory leak messages for iterators that have
- * # not been fully consumed
- * if self.pileup_iter != <bam_plp_t>NULL: # <<<<<<<<<<<<<<
- * bam_plp_reset(self.pileup_iter)
- * bam_plp_destroy(self.pileup_iter)
+ /* "csamtools.pyx":1620
+ * """
+ * # Create an initial iterator
+ * if self.tid==-1: # <<<<<<<<<<<<<<
+ * if not self.samfile.nreferences:
+ * raise StopIteration
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter != ((bam_plp_t)NULL));
+ __pyx_t_1 = (__pyx_v_self->tid == -1);
if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1704
- * # not been fully consumed
- * if self.pileup_iter != <bam_plp_t>NULL:
- * bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
- * bam_plp_destroy(self.pileup_iter)
- * self.pileup_iter = <bam_plp_t>NULL
+ /* "csamtools.pyx":1621
+ * # Create an initial iterator
+ * if self.tid==-1:
+ * if not self.samfile.nreferences: # <<<<<<<<<<<<<<
+ * raise StopIteration
+ * self.tid = 0
*/
- bam_plp_reset(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = (!__pyx_t_1);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1705
- * if self.pileup_iter != <bam_plp_t>NULL:
- * bam_plp_reset(self.pileup_iter)
- * bam_plp_destroy(self.pileup_iter) # <<<<<<<<<<<<<<
- * self.pileup_iter = <bam_plp_t>NULL
+ /* "csamtools.pyx":1622
+ * if self.tid==-1:
+ * if not self.samfile.nreferences:
+ * raise StopIteration # <<<<<<<<<<<<<<
+ * self.tid = 0
+ * self.nextiter()
+ */
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+
+ /* "csamtools.pyx":1623
+ * if not self.samfile.nreferences:
+ * raise StopIteration
+ * self.tid = 0 # <<<<<<<<<<<<<<
+ * self.nextiter()
*
*/
- bam_plp_destroy(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
+ __pyx_v_self->tid = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1706
- * bam_plp_reset(self.pileup_iter)
- * bam_plp_destroy(self.pileup_iter)
- * self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1624
+ * raise StopIteration
+ * self.tid = 0
+ * self.nextiter() # <<<<<<<<<<<<<<
*
- * if self.iterdata.seq != NULL:
+ * while 1:
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
- goto __pyx_L5;
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1708
- * self.pileup_iter = <bam_plp_t>NULL
+ /* "csamtools.pyx":1626
+ * self.nextiter()
+ *
+ * while 1: # <<<<<<<<<<<<<<
+ * self.rowiter.cnext()
*
- * if self.iterdata.seq != NULL: # <<<<<<<<<<<<<<
- * free(self.iterdata.seq)
- * self.iterdata.seq = NULL
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
- if (__pyx_t_1) {
+ while (1) {
+ if (!1) break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1709
+ /* "csamtools.pyx":1627
*
- * if self.iterdata.seq != NULL:
- * free(self.iterdata.seq) # <<<<<<<<<<<<<<
- * self.iterdata.seq = NULL
+ * while 1:
+ * self.rowiter.cnext() # <<<<<<<<<<<<<<
*
+ * # If current iterator is not exhausted, return aligned read
*/
- free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
+ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)__pyx_v_self->rowiter->__pyx_vtab)->cnext(__pyx_v_self->rowiter);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1710
- * if self.iterdata.seq != NULL:
- * free(self.iterdata.seq)
- * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1630
+ *
+ * # If current iterator is not exhausted, return aligned read
+ * if self.rowiter.retval>0: # <<<<<<<<<<<<<<
+ * return makeAlignedRead(self.rowiter.b)
*
- * cdef class IteratorColumnRegion(IteratorColumn):
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_3 = (__pyx_v_self->rowiter->retval > 0);
+ if (__pyx_t_3) {
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
+ /* "csamtools.pyx":1631
+ * # If current iterator is not exhausted, return aligned read
+ * if self.rowiter.retval>0:
+ * return makeAlignedRead(self.rowiter.b) # <<<<<<<<<<<<<<
+ *
+ * self.tid += 1
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_4 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_r = __pyx_t_4;
+ __pyx_t_4 = 0;
+ goto __pyx_L0;
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1715
- * '''iterates over a region only.
- * '''
- * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
- * int tid = 0,
- * int start = 0,
+ /* "csamtools.pyx":1633
+ * return makeAlignedRead(self.rowiter.b)
+ *
+ * self.tid += 1 # <<<<<<<<<<<<<<
+ *
+ * # Otherwise, proceed to next reference or stop
*/
+ __pyx_v_self->tid = (__pyx_v_self->tid + 1);
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- int __pyx_v_tid;
- int __pyx_v_start;
- int __pyx_v_end;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1715);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[4] = {0,0,0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (value) { values[3] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1715; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- if (values[1]) {
- __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1716; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else {
- __pyx_v_tid = ((int)0);
- }
- if (values[2]) {
- __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1717; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else {
- __pyx_v_start = ((int)0);
- }
- if (values[3]) {
- __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else {
- __pyx_v_end = __pyx_k_58;
- }
- } else {
- __pyx_v_tid = ((int)0);
- __pyx_v_start = ((int)0);
- __pyx_v_end = __pyx_k_58;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: __pyx_v_end = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 3)); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 3: __pyx_v_start = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 2)); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1717; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 2: __pyx_v_tid = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1716; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 1: __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
- break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1715; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1722
- *
- * # initialize iterator
- * self.setupIteratorData( tid, start, end, 1 ) # <<<<<<<<<<<<<<
- *
- * def __next__(self):
- */
- __pyx_t_2.__pyx_n = 1;
- __pyx_t_2.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1724
- * self.setupIteratorData( tid, start, end, 1 )
- *
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
- * """
- */
-
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_20IteratorColumnRegion___next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__;
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion___next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1724);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1728
- * """
- *
- * while 1: # <<<<<<<<<<<<<<
- * self.cnext()
- * if self.n_plp < 0:
- */
- while (1) {
- if (!1) break;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1729
- *
- * while 1:
- * self.cnext() # <<<<<<<<<<<<<<
- * if self.n_plp < 0:
- * raise ValueError("error during iteration" )
- */
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1730
- * while 1:
- * self.cnext()
- * if self.n_plp < 0: # <<<<<<<<<<<<<<
- * raise ValueError("error during iteration" )
+ /* "csamtools.pyx":1636
*
+ * # Otherwise, proceed to next reference or stop
+ * if self.tid<self.samfile.nreferences: # <<<<<<<<<<<<<<
+ * self.nextiter()
+ * else:
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp < 0);
- if (__pyx_t_1) {
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1731
- * self.cnext()
- * if self.n_plp < 0:
- * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
- *
- * if self.plp == NULL:
+ /* "csamtools.pyx":1637
+ * # Otherwise, proceed to next reference or stop
+ * if self.tid<self.samfile.nreferences:
+ * self.nextiter() # <<<<<<<<<<<<<<
+ * else:
+ * raise StopIteration
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_59));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_59));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_59));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ goto __pyx_L8;
}
- __pyx_L7:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1733
- * raise ValueError("error during iteration" )
- *
- * if self.plp == NULL: # <<<<<<<<<<<<<<
- * raise StopIteration
- *
- */
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp == NULL);
- if (__pyx_t_1) {
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1734
- *
- * if self.plp == NULL:
+ /* "csamtools.pyx":1639
+ * self.nextiter()
+ * else:
* raise StopIteration # <<<<<<<<<<<<<<
*
- * return makePileupProxy( <bam_pileup1_t*>self.plp,
+ * cdef class IteratorRowSelection(IteratorRow):
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L8:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1736
- * raise StopIteration
- *
- * return makePileupProxy( <bam_pileup1_t*>self.plp, # <<<<<<<<<<<<<<
- * self.tid,
- * self.pos,
- */
- __Pyx_XDECREF(__pyx_r);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1739
- * self.tid,
- * self.pos,
- * self.n_plp ) # <<<<<<<<<<<<<<
- *
- * cdef class IteratorColumnAllRefs(IteratorColumn):
- */
- __pyx_t_3 = __pyx_f_9csamtools_makePileupProxy(((bam_pileup1_t *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__next__");
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1745
+/* Python wrapper */
+static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ PyObject *__pyx_v_positions = 0;
+ int __pyx_v_reopen;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ {
+ PyObject* values[3] = {0,0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__positions);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ if (values[2]) {
+ } else {
+
+ /* "csamtools.pyx":1647
* """
*
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * Samfile samfile,
- * **kwargs ):
+ * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
*/
-
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- int __pyx_t_3;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1745);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_reopen = ((int)1);
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
}
__pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
+ __pyx_v_positions = values[1];
+ if (values[2]) {
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_reopen = ((int)1);
+ }
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__");
+ __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1750
- *
- * # no iteration over empty files
- * if not samfile.nreferences: raise StopIteration # <<<<<<<<<<<<<<
- *
- * # initialize iterator
- */
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = (!__pyx_t_2);
- if (__pyx_t_3) {
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1753
- *
- * # initialize iterator
- * self.setupIteratorData( self.tid, 0, max_pos, 1 ) # <<<<<<<<<<<<<<
- *
- * def __next__(self):
- */
- __pyx_t_4.__pyx_n = 1;
- __pyx_t_4.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- __pyx_r = 0;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self), __pyx_v_samfile, __pyx_v_positions, __pyx_v_reopen);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__");
__pyx_r = -1;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1755
- * self.setupIteratorData( self.tid, 0, max_pos, 1 )
- *
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
- * """
- */
-
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_21IteratorColumnAllRefs___next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__;
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs___next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
+static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_5;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1755);
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1759
- * """
+ /* "csamtools.pyx":1649
+ * def __cinit__(self, Samfile samfile, positions, int reopen = True ):
*
- * while 1: # <<<<<<<<<<<<<<
- * self.cnext()
+ * if not samfile._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
*
*/
- while (1) {
- if (!1) break;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = (!__pyx_t_3);
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1760
+ /* "csamtools.pyx":1650
*
- * while 1:
- * self.cnext() # <<<<<<<<<<<<<<
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
- * if self.n_plp < 0:
+ * if not samfile._isOpen():
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_123), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1762
- * self.cnext()
+ /* "csamtools.pyx":1652
+ * raise ValueError( "I/O operation on closed file" )
*
- * if self.n_plp < 0: # <<<<<<<<<<<<<<
- * raise ValueError("error during iteration" )
+ * if not samfile._isOpen(): # <<<<<<<<<<<<<<
+ * raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp < 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = (!__pyx_t_4);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1763
+ /* "csamtools.pyx":1653
*
- * if self.n_plp < 0:
- * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
- * # return result, if within same reference
+ * assert samfile.isbam, "can only use this iterator on bam files"
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_59));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_59));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_59));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
- }
- __pyx_L7:;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_124), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1766
+ /* "csamtools.pyx":1655
+ * raise ValueError( "I/O operation on closed file" )
+ *
+ * assert samfile.isbam, "can only use this iterator on bam files" # <<<<<<<<<<<<<<
+ * mode = b"rb"
*
- * # return result, if within same reference
- * if self.plp != NULL: # <<<<<<<<<<<<<<
- * return makePileupProxy( <bam_pileup1_t*>self.plp,
- * self.tid,
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp != NULL);
- if (__pyx_t_1) {
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!__pyx_v_samfile->isbam)) {
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_125));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1767
- * # return result, if within same reference
- * if self.plp != NULL:
- * return makePileupProxy( <bam_pileup1_t*>self.plp, # <<<<<<<<<<<<<<
- * self.tid,
- * self.pos,
+ /* "csamtools.pyx":1656
+ *
+ * assert samfile.isbam, "can only use this iterator on bam files"
+ * mode = b"rb" # <<<<<<<<<<<<<<
+ *
+ * # reopen the file to avoid iterator conflict
*/
- __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
+ __pyx_v_mode = __pyx_n_b__rb;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1770
- * self.tid,
- * self.pos,
- * self.n_plp ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1659
*
- * # otherwise, proceed to next reference or stop
+ * # reopen the file to avoid iterator conflict
+ * if reopen: # <<<<<<<<<<<<<<
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
*/
- __pyx_t_3 = __pyx_f_9csamtools_makePileupProxy(((bam_pileup1_t *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
- goto __pyx_L8;
- }
- __pyx_L8:;
+ if (__pyx_v_reopen) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1773
- *
- * # otherwise, proceed to next reference or stop
- * self.tid += 1 # <<<<<<<<<<<<<<
- * if self.tid < self.samfile.nreferences:
- * self.setupIteratorData( self.tid, 0, max_pos, 0 )
+ /* "csamtools.pyx":1660
+ * # reopen the file to avoid iterator conflict
+ * if reopen:
+ * store = StderrStore() # <<<<<<<<<<<<<<
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_store = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":1661
+ * if reopen:
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
+ * store.release()
+ * assert self.fp != NULL
*/
- ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid += 1;
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1774
- * # otherwise, proceed to next reference or stop
- * self.tid += 1
- * if self.tid < self.samfile.nreferences: # <<<<<<<<<<<<<<
- * self.setupIteratorData( self.tid, 0, max_pos, 0 )
- * else:
+ /* "csamtools.pyx":1662
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release() # <<<<<<<<<<<<<<
+ * assert self.fp != NULL
+ * self.owns_samfile = True
*/
- __pyx_t_3 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_1) {
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1775
- * self.tid += 1
- * if self.tid < self.samfile.nreferences:
- * self.setupIteratorData( self.tid, 0, max_pos, 0 ) # <<<<<<<<<<<<<<
- * else:
- * raise StopIteration
+ /* "csamtools.pyx":1663
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ * assert self.fp != NULL # <<<<<<<<<<<<<<
+ * self.owns_samfile = True
+ * else:
*/
- __pyx_t_5.__pyx_n = 1;
- __pyx_t_5.reopen = 0;
- __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L9;
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ PyErr_SetNone(PyExc_AssertionError);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /*else*/ {
+ #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1777
- * self.setupIteratorData( self.tid, 0, max_pos, 0 )
- * else:
- * raise StopIteration # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1664
+ * store.release()
+ * assert self.fp != NULL
+ * self.owns_samfile = True # <<<<<<<<<<<<<<
+ * else:
+ * self.fp = samfile.samfile
+ */
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L5;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":1666
+ * self.owns_samfile = True
+ * else:
+ * self.fp = samfile.samfile # <<<<<<<<<<<<<<
+ * self.owns_samfile = False
*
- * ##-------------------------------------------------------------------
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_L9:;
+ __pyx_v_self->fp = __pyx_v_samfile->samfile;
+
+ /* "csamtools.pyx":1667
+ * else:
+ * self.fp = samfile.samfile
+ * self.owns_samfile = False # <<<<<<<<<<<<<<
+ *
+ * # allocate memory for alignment
+ */
+ __pyx_v_self->owns_samfile = 0;
}
+ __pyx_L5:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":1670
+ *
+ * # allocate memory for alignment
+ * self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
+ *
+ * self.positions = positions
+ */
+ __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+
+ /* "csamtools.pyx":1672
+ * self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
+ *
+ * self.positions = positions # <<<<<<<<<<<<<<
+ * self.current_pos = 0
+ *
+ */
+ __Pyx_INCREF(__pyx_v_positions);
+ __Pyx_GIVEREF(__pyx_v_positions);
+ __Pyx_GOTREF(__pyx_v_self->positions);
+ __Pyx_DECREF(__pyx_v_self->positions);
+ __pyx_v_self->positions = __pyx_v_positions;
+
+ /* "csamtools.pyx":1673
+ *
+ * self.positions = positions
+ * self.current_pos = 0 # <<<<<<<<<<<<<<
+ *
+ * def __iter__(self):
+ */
+ __pyx_v_self->current_pos = 0;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__next__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_XDECREF(__pyx_v_mode);
+ __Pyx_XDECREF(__pyx_v_store);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1782
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
- * cdef inline int32_t query_start(bam1_t *src) except -1: # <<<<<<<<<<<<<<
- * cdef uint32_t * cigar_p, op
- * cdef uint32_t k
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1675
+ * self.current_pos = 0
+ *
+ * def __iter__(self): # <<<<<<<<<<<<<<
+ * return self
+ *
*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) {
- uint32_t *__pyx_v_cigar_p;
- uint32_t __pyx_v_op;
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_start_offset;
- int32_t __pyx_r;
- uint32_t __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
- int __pyx_t_4;
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_start");
- __Pyx_TraceCall("query_start", __pyx_f[0], 1782);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1675);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1785
- * cdef uint32_t * cigar_p, op
- * cdef uint32_t k
- * cdef uint32_t start_offset = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1676
*
- * if src.core.n_cigar:
+ * def __iter__(self):
+ * return self # <<<<<<<<<<<<<<
+ *
+ * cdef bam1_t * getCurrent( self ):
*/
- __pyx_v_start_offset = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1787
- * cdef uint32_t start_offset = 0
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1678
+ * return self
+ *
+ * cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
+ * return self.b
*
- * if src.core.n_cigar: # <<<<<<<<<<<<<<
- * cigar_p = bam1_cigar(src);
- * for k from 0 <= k < src.core.n_cigar:
*/
- if (__pyx_v_src->core.n_cigar) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1788
- *
- * if src.core.n_cigar:
- * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
- */
- __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1789
- * if src.core.n_cigar:
- * cigar_p = bam1_cigar(src);
- * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * if op==BAM_CHARD_CLIP:
- */
- __pyx_t_1 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1790
- * cigar_p = bam1_cigar(src);
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
- * if op==BAM_CHARD_CLIP:
- * if start_offset!=0 and start_offset!=src.core.l_qseq:
- */
- __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1791
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
- * if start_offset!=0 and start_offset!=src.core.l_qseq:
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- */
- switch (__pyx_v_op) {
- case 5:
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1792
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * if op==BAM_CHARD_CLIP:
- * if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- * return -1
- */
- __pyx_t_2 = (__pyx_v_start_offset != 0);
- if (__pyx_t_2) {
- __pyx_t_3 = (__pyx_v_start_offset != __pyx_v_src->core.l_qseq);
- __pyx_t_4 = __pyx_t_3;
- } else {
- __pyx_t_4 = __pyx_t_2;
- }
- if (__pyx_t_4) {
+static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+ bam1_t *__pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1678);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1793
- * if op==BAM_CHARD_CLIP:
- * if start_offset!=0 and start_offset!=src.core.l_qseq:
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
- * return -1
- * elif op==BAM_CSOFT_CLIP:
+ /* "csamtools.pyx":1679
+ *
+ * cdef bam1_t * getCurrent( self ):
+ * return self.b # <<<<<<<<<<<<<<
+ *
+ * cdef int cnext(self):
*/
- PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_60);
+ __pyx_r = __pyx_v_self->b;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1794
- * if start_offset!=0 and start_offset!=src.core.l_qseq:
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- * return -1 # <<<<<<<<<<<<<<
- * elif op==BAM_CSOFT_CLIP:
- * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
- */
- __pyx_r = -1;
- goto __pyx_L0;
- goto __pyx_L6;
- }
- __pyx_L6:;
- break;
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1795
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- * return -1
- * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
- * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
- * else:
+/* "csamtools.pyx":1681
+ * return self.b
+ *
+ * cdef int cnext(self): # <<<<<<<<<<<<<<
+ * '''cversion of iterator'''
+ *
*/
- case 4:
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1796
- * return -1
- * elif op==BAM_CSOFT_CLIP:
- * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
- * else:
- * break
- */
- __pyx_v_start_offset += ((__pyx_v_cigar_p[__pyx_v_k]) >> 4);
- break;
- default:
+static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ Py_ssize_t __pyx_t_2;
+ int __pyx_t_3;
+ uint64_t __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1681);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1798
- * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
- * else:
- * break # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1685
*
- * return start_offset
+ * # end iteration if out of positions
+ * if self.current_pos >= len(self.positions): return -1 # <<<<<<<<<<<<<<
+ *
+ * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
*/
- goto __pyx_L5_break;
- break;
- }
- }
- __pyx_L5_break:;
+ __pyx_t_1 = __pyx_v_self->positions;
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = (__pyx_v_self->current_pos >= __pyx_t_2);
+ if (__pyx_t_3) {
+ __pyx_r = -1;
+ goto __pyx_L0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1800
- * break
+ /* "csamtools.pyx":1687
+ * if self.current_pos >= len(self.positions): return -1
*
- * return start_offset # <<<<<<<<<<<<<<
+ * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) # <<<<<<<<<<<<<<
+ * self.current_pos += 1
+ * return samread(self.fp, self.b)
+ */
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_self->positions, __pyx_v_self->current_pos, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = __Pyx_PyInt_from_py_uint64_t(__pyx_t_1); if (unlikely((__pyx_t_4 == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ bam_seek(__pyx_v_self->fp->x.bam, __pyx_t_4, 0);
+
+ /* "csamtools.pyx":1688
+ *
+ * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
+ * self.current_pos += 1 # <<<<<<<<<<<<<<
+ * return samread(self.fp, self.b)
*
- * ##-------------------------------------------------------------------
*/
- __pyx_r = __pyx_v_start_offset;
+ __pyx_v_self->current_pos = (__pyx_v_self->current_pos + 1);
+
+ /* "csamtools.pyx":1689
+ * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
+ * self.current_pos += 1
+ * return samread(self.fp, self.b) # <<<<<<<<<<<<<<
+ *
+ * def __next__(self):
+ */
+ __pyx_r = samread(__pyx_v_self->fp, __pyx_v_self->b);
goto __pyx_L0;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_WriteUnraisable("csamtools.IteratorRowSelection.cnext", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1805
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
- * cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
- * cdef uint32_t * cigar_p, op
- * cdef uint32_t k
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_20IteratorRowSelection_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__;
+static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_20IteratorRowSelection_4__next__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1691
+ * return samread(self.fp, self.b)
+ *
+ * def __next__(self): # <<<<<<<<<<<<<<
+ * """python version of next().
+ *
*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
- uint32_t *__pyx_v_cigar_p;
- uint32_t __pyx_v_op;
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_end_offset;
- int32_t __pyx_r;
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+ int __pyx_v_ret;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
- int __pyx_t_2;
- int __pyx_t_3;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_end");
- __Pyx_TraceCall("query_end", __pyx_f[0], 1805);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1691);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1808
- * cdef uint32_t * cigar_p, op
- * cdef uint32_t k
- * cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1697
+ * """
*
- * if src.core.n_cigar>1:
+ * cdef int ret = self.cnext() # <<<<<<<<<<<<<<
+ * if (ret > 0):
+ * return makeAlignedRead( self.b )
*/
- __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
+ __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1810
- * cdef uint32_t end_offset = src.core.l_qseq
+ /* "csamtools.pyx":1698
*
- * if src.core.n_cigar>1: # <<<<<<<<<<<<<<
- * cigar_p = bam1_cigar(src);
- * for k from src.core.n_cigar > k >= 1:
+ * cdef int ret = self.cnext()
+ * if (ret > 0): # <<<<<<<<<<<<<<
+ * return makeAlignedRead( self.b )
+ * else:
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar > 1);
+ __pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1811
- *
- * if src.core.n_cigar>1:
- * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
- * for k from src.core.n_cigar > k >= 1:
- * op = cigar_p[k] & BAM_CIGAR_MASK
+ /* "csamtools.pyx":1699
+ * cdef int ret = self.cnext()
+ * if (ret > 0):
+ * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
+ * else:
+ * raise StopIteration
*/
- __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1812
- * if src.core.n_cigar>1:
- * cigar_p = bam1_cigar(src);
- * for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<<
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * if op==BAM_CHARD_CLIP:
+ /* "csamtools.pyx":1701
+ * return makeAlignedRead( self.b )
+ * else:
+ * raise StopIteration # <<<<<<<<<<<<<<
+ *
+ * def __dealloc__(self):
*/
- for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1813
- * cigar_p = bam1_cigar(src);
- * for k from src.core.n_cigar > k >= 1:
- * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
- * if op==BAM_CHARD_CLIP:
- * if end_offset!=0 and end_offset!=src.core.l_qseq:
- */
- __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorRowSelection.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1814
- * for k from src.core.n_cigar > k >= 1:
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
- * if end_offset!=0 and end_offset!=src.core.l_qseq:
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- */
- switch (__pyx_v_op) {
- case 5:
+/* Python wrapper */
+static void __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1815
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * if op==BAM_CHARD_CLIP:
- * if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- * return -1
- */
- __pyx_t_1 = (__pyx_v_end_offset != 0);
- if (__pyx_t_1) {
- __pyx_t_2 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
- __pyx_t_3 = __pyx_t_2;
- } else {
- __pyx_t_3 = __pyx_t_1;
- }
- if (__pyx_t_3) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1816
- * if op==BAM_CHARD_CLIP:
- * if end_offset!=0 and end_offset!=src.core.l_qseq:
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
- * return -1
- * elif op==BAM_CSOFT_CLIP:
- */
- PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_60);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1817
- * if end_offset!=0 and end_offset!=src.core.l_qseq:
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- * return -1 # <<<<<<<<<<<<<<
- * elif op==BAM_CSOFT_CLIP:
- * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
+/* "csamtools.pyx":1703
+ * raise StopIteration
+ *
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * bam_destroy1(self.b)
+ * if self.owns_samfile: samclose( self.fp )
*/
- __pyx_r = -1;
- goto __pyx_L0;
- goto __pyx_L6;
- }
- __pyx_L6:;
- break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1818
- * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
- * return -1
- * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
- * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
- * else:
- */
- case 4:
+static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1703);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1819
- * return -1
- * elif op==BAM_CSOFT_CLIP:
- * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
- * else:
- * break
+ /* "csamtools.pyx":1704
+ *
+ * def __dealloc__(self):
+ * bam_destroy1(self.b) # <<<<<<<<<<<<<<
+ * if self.owns_samfile: samclose( self.fp )
+ *
*/
- __pyx_v_end_offset -= ((__pyx_v_cigar_p[__pyx_v_k]) >> 4);
- break;
- default:
+ bam_destroy1(__pyx_v_self->b);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1821
- * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
- * else:
- * break # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1705
+ * def __dealloc__(self):
+ * bam_destroy1(self.b)
+ * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
- * if end_offset==0:
+ * ##-------------------------------------------------------------------
*/
- goto __pyx_L5_break;
- break;
- }
- }
- __pyx_L5_break:;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
goto __pyx_L3;
}
__pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1823
- * break
- *
- * if end_offset==0: # <<<<<<<<<<<<<<
- * end_offset = src.core.l_qseq
- *
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "csamtools.pyx":1710
+ * ##-------------------------------------------------------------------
+ * ##-------------------------------------------------------------------
+ * cdef int __advance_all( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
+ * '''advance without any read filtering.
+ * '''
*/
- __pyx_t_3 = (__pyx_v_end_offset == 0);
- if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1824
- *
- * if end_offset==0:
- * end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
+static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_9csamtools___iterdata *__pyx_v_d;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__advance_all", 0);
+ __Pyx_TraceCall("__advance_all", __pyx_f[0], 1710);
+
+ /* "csamtools.pyx":1714
+ * '''
+ * cdef __iterdata * d
+ * d = <__iterdata*>data # <<<<<<<<<<<<<<
+ * return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
- * return end_offset
*/
- __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
- goto __pyx_L7;
- }
- __pyx_L7:;
+ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1826
- * end_offset = src.core.l_qseq
- *
- * return end_offset # <<<<<<<<<<<<<<
- *
+ /* "csamtools.pyx":1715
+ * cdef __iterdata * d
+ * d = <__iterdata*>data
+ * return bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
*
+ * cdef int __advance_snpcalls( void * data, bam1_t * b ):
*/
- __pyx_r = __pyx_v_end_offset;
+ __pyx_r = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
goto __pyx_L0;
__pyx_r = 0;
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1829
- *
+/* "csamtools.pyx":1717
+ * return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
- * cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
- * cdef uint8_t * p
- * cdef uint32_t k
+ * cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
+ * '''advance using same filter and read processing as in
+ * the samtools pileup.
*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
- uint8_t *__pyx_v_p;
- uint32_t __pyx_v_k;
- char *__pyx_v_s;
- PyObject *__pyx_v_seq;
- PyObject *__pyx_r = NULL;
+static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_9csamtools___iterdata *__pyx_v_d;
+ int __pyx_v_ret;
+ int __pyx_v_skip;
+ int __pyx_v_q;
+ int __pyx_v_is_cns;
+ int __pyx_v_is_nobaq;
+ int __pyx_v_capQ_thres;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- uint32_t __pyx_t_3;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ long __pyx_t_7;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_seq_range");
- __Pyx_TraceCall("get_seq_range", __pyx_f[0], 1829);
- __pyx_v_seq = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("__advance_snpcalls", 0);
+ __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1717);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1834
- * cdef char * s
- *
- * if not src.core.l_qseq: # <<<<<<<<<<<<<<
- * return None
+ /* "csamtools.pyx":1722
+ * '''
+ * cdef __iterdata * d
+ * d = <__iterdata*>data # <<<<<<<<<<<<<<
*
+ * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*/
- __pyx_t_1 = (!__pyx_v_src->core.l_qseq);
- if (__pyx_t_1) {
+ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1835
- *
- * if not src.core.l_qseq:
- * return None # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1724
+ * d = <__iterdata*>data
*
- * seq = PyString_FromStringAndSize(NULL, end-start)
+ * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
+ * cdef int skip = 0
+ * cdef int q
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L3;
- }
- __pyx_L3:;
+ __pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1837
- * return None
+ /* "csamtools.pyx":1725
*
- * seq = PyString_FromStringAndSize(NULL, end-start) # <<<<<<<<<<<<<<
- * s = PyString_AS_STRING(seq)
- * p = bam1_seq(src)
+ * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
+ * cdef int skip = 0 # <<<<<<<<<<<<<<
+ * cdef int q
+ * cdef int is_cns = 1
*/
- __pyx_t_2 = PyString_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_seq);
- __pyx_v_seq = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_skip = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1838
- *
- * seq = PyString_FromStringAndSize(NULL, end-start)
- * s = PyString_AS_STRING(seq) # <<<<<<<<<<<<<<
- * p = bam1_seq(src)
- *
+ /* "csamtools.pyx":1727
+ * cdef int skip = 0
+ * cdef int q
+ * cdef int is_cns = 1 # <<<<<<<<<<<<<<
+ * cdef int is_nobaq = 0
+ * cdef int capQ_thres = 0
*/
- __pyx_v_s = PyString_AS_STRING(__pyx_v_seq);
+ __pyx_v_is_cns = 1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1839
- * seq = PyString_FromStringAndSize(NULL, end-start)
- * s = PyString_AS_STRING(seq)
- * p = bam1_seq(src) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1728
+ * cdef int q
+ * cdef int is_cns = 1
+ * cdef int is_nobaq = 0 # <<<<<<<<<<<<<<
+ * cdef int capQ_thres = 0
*
- * for k from start <= k < end:
*/
- __pyx_v_p = bam1_seq(__pyx_v_src);
+ __pyx_v_is_nobaq = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1841
- * p = bam1_seq(src)
+ /* "csamtools.pyx":1729
+ * cdef int is_cns = 1
+ * cdef int is_nobaq = 0
+ * cdef int capQ_thres = 0 # <<<<<<<<<<<<<<
*
- * for k from start <= k < end: # <<<<<<<<<<<<<<
- * # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
- * # note: do not use string literal as it will be a python string
+ * # reload sequence
*/
- __pyx_t_3 = __pyx_v_end;
- for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
+ __pyx_v_capQ_thres = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1844
- * # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
- * # note: do not use string literal as it will be a python string
- * s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1732
*
- * return seq
+ * # reload sequence
+ * if d.fastafile != NULL and b.core.tid != d.tid: # <<<<<<<<<<<<<<
+ * if d.seq != NULL: free(d.seq)
+ * d.tid = b.core.tid
*/
- (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
+ __pyx_t_1 = (__pyx_v_d->fastafile != NULL);
+ if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_b->core.tid != __pyx_v_d->tid);
+ __pyx_t_3 = __pyx_t_2;
+ } else {
+ __pyx_t_3 = __pyx_t_1;
}
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1846
- * s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf]
- *
- * return seq # <<<<<<<<<<<<<<
- *
- *
+ /* "csamtools.pyx":1733
+ * # reload sequence
+ * if d.fastafile != NULL and b.core.tid != d.tid:
+ * if d.seq != NULL: free(d.seq) # <<<<<<<<<<<<<<
+ * d.tid = b.core.tid
+ * d.seq = faidx_fetch_seq(d.fastafile,
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_seq);
- __pyx_r = __pyx_v_seq;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.get_seq_range");
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_seq);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_3 = (__pyx_v_d->seq != NULL);
+ if (__pyx_t_3) {
+ free(__pyx_v_d->seq);
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1849
- *
- *
- * cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
- * cdef uint8_t * p
- * cdef uint32_t k
+ /* "csamtools.pyx":1734
+ * if d.fastafile != NULL and b.core.tid != d.tid:
+ * if d.seq != NULL: free(d.seq)
+ * d.tid = b.core.tid # <<<<<<<<<<<<<<
+ * d.seq = faidx_fetch_seq(d.fastafile,
+ * d.samfile.header.target_name[d.tid],
*/
+ __pyx_v_d->tid = __pyx_v_b->core.tid;
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
- uint8_t *__pyx_v_p;
- uint32_t __pyx_v_k;
- char *__pyx_v_q;
- PyObject *__pyx_v_qual;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- uint32_t __pyx_t_3;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_qual_range");
- __Pyx_TraceCall("get_qual_range", __pyx_f[0], 1849);
- __pyx_v_qual = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":1735
+ * if d.seq != NULL: free(d.seq)
+ * d.tid = b.core.tid
+ * d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<<
+ * d.samfile.header.target_name[d.tid],
+ * 0, max_pos,
+ */
+ __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_9csamtools_max_pos, (&__pyx_v_d->seq_len));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1854
- * cdef char * q
- *
- * p = bam1_qual(src) # <<<<<<<<<<<<<<
- * if p[0] == 0xff:
- * return None
+ /* "csamtools.pyx":1739
+ * 0, max_pos,
+ * &d.seq_len)
+ * if d.seq == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
+ * (d.samfile.header.target_name[d.tid],
*/
- __pyx_v_p = bam1_qual(__pyx_v_src);
+ __pyx_t_3 = (__pyx_v_d->seq == NULL);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1855
- *
- * p = bam1_qual(src)
- * if p[0] == 0xff: # <<<<<<<<<<<<<<
- * return None
+ /* "csamtools.pyx":1741
+ * if d.seq == NULL:
+ * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
+ * (d.samfile.header.target_name[d.tid], # <<<<<<<<<<<<<<
+ * d.tid))
*
*/
- __pyx_t_1 = ((__pyx_v_p[0]) == 0xff);
- if (__pyx_t_1) {
+ __pyx_t_4 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1856
- * p = bam1_qual(src)
- * if p[0] == 0xff:
- * return None # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1742
+ * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
+ * (d.samfile.header.target_name[d.tid],
+ * d.tid)) # <<<<<<<<<<<<<<
+ *
*
- * qual = PyString_FromStringAndSize(NULL, end-start)
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_4 = 0;
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_126), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
goto __pyx_L3;
}
__pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1858
- * return None
+ /* "csamtools.pyx":1745
*
- * qual = PyString_FromStringAndSize(NULL, end-start) # <<<<<<<<<<<<<<
- * q = PyString_AS_STRING(qual)
*
+ * while ret >= 0: # <<<<<<<<<<<<<<
+ *
+ * skip = 0
*/
- __pyx_t_2 = PyString_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_qual);
- __pyx_v_qual = __pyx_t_2;
- __pyx_t_2 = 0;
+ while (1) {
+ __pyx_t_3 = (__pyx_v_ret >= 0);
+ if (!__pyx_t_3) break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1859
+ /* "csamtools.pyx":1747
+ * while ret >= 0:
*
- * qual = PyString_FromStringAndSize(NULL, end-start)
- * q = PyString_AS_STRING(qual) # <<<<<<<<<<<<<<
+ * skip = 0 # <<<<<<<<<<<<<<
*
- * for k from start <= k < end:
+ * # realign read - changes base qualities
*/
- __pyx_v_q = PyString_AS_STRING(__pyx_v_qual);
+ __pyx_v_skip = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1861
- * q = PyString_AS_STRING(qual)
+ /* "csamtools.pyx":1750
*
- * for k from start <= k < end: # <<<<<<<<<<<<<<
- * ## equivalent to t[i] + 33 (see bam.c)
- * q[k-start] = p[k] + 33
- */
- __pyx_t_3 = __pyx_v_end;
- for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1863
- * for k from start <= k < end:
- * ## equivalent to t[i] + 33 (see bam.c)
- * q[k-start] = p[k] + 33 # <<<<<<<<<<<<<<
+ * # realign read - changes base qualities
+ * if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq ) # <<<<<<<<<<<<<<
*
- * return qual
+ * if d.seq != NULL and capQ_thres > 10:
*/
- (__pyx_v_q[(__pyx_v_k - __pyx_v_start)]) = ((__pyx_v_p[__pyx_v_k]) + 33);
- }
+ __pyx_t_3 = (__pyx_v_d->seq != NULL);
+ if (__pyx_t_3) {
+ if (__pyx_v_is_cns) {
+ __pyx_t_1 = (!__pyx_v_is_nobaq);
+ __pyx_t_2 = __pyx_t_1;
+ } else {
+ __pyx_t_2 = __pyx_v_is_cns;
+ }
+ __pyx_t_1 = __pyx_t_2;
+ } else {
+ __pyx_t_1 = __pyx_t_3;
+ }
+ if (__pyx_t_1) {
+ bam_prob_realn(__pyx_v_b, __pyx_v_d->seq);
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1865
- * q[k-start] = p[k] + 33
- *
- * return qual # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1752
+ * if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq )
*
- * cdef class AlignedRead:
+ * if d.seq != NULL and capQ_thres > 10: # <<<<<<<<<<<<<<
+ * q = bam_cap_mapQ(b, d.seq, capQ_thres)
+ * if q < 0: skip = 1
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_qual);
- __pyx_r = __pyx_v_qual;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.get_qual_range");
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_qual);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_1 = (__pyx_v_d->seq != NULL);
+ if (__pyx_t_1) {
+ __pyx_t_3 = (__pyx_v_capQ_thres > 10);
+ __pyx_t_2 = __pyx_t_3;
+ } else {
+ __pyx_t_2 = __pyx_t_1;
+ }
+ if (__pyx_t_2) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1890
+ /* "csamtools.pyx":1753
*
- * # Now only called when instances are created from Python
- * def __init__(self): # <<<<<<<<<<<<<<
- * # see bam_init1
- * self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) )
+ * if d.seq != NULL and capQ_thres > 10:
+ * q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
+ * if q < 0: skip = 1
+ * elif b.core.qual > q: b.core.qual = q
*/
+ __pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
-static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 1890);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1892
- * def __init__(self):
- * # see bam_init1
- * self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
- * # allocate some memory
- * # If size is 0, calloc does not return a pointer that can be passed to free()
+ /* "csamtools.pyx":1754
+ * if d.seq != NULL and capQ_thres > 10:
+ * q = bam_cap_mapQ(b, d.seq, capQ_thres)
+ * if q < 0: skip = 1 # <<<<<<<<<<<<<<
+ * elif b.core.qual > q: b.core.qual = q
+ * if b.core.flag & BAM_FUNMAP: skip = 1
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ __pyx_t_2 = (__pyx_v_q < 0);
+ if (__pyx_t_2) {
+ __pyx_v_skip = 1;
+ goto __pyx_L10;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1896
- * # If size is 0, calloc does not return a pointer that can be passed to free()
- * # so allocate 40 bytes for a new read
- * self._delegate.m_data = 40 # <<<<<<<<<<<<<<
- * self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
- * self._delegate.data_len = 0
+ /* "csamtools.pyx":1755
+ * q = bam_cap_mapQ(b, d.seq, capQ_thres)
+ * if q < 0: skip = 1
+ * elif b.core.qual > q: b.core.qual = q # <<<<<<<<<<<<<<
+ * if b.core.flag & BAM_FUNMAP: skip = 1
+ * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data = 40;
+ __pyx_t_2 = (__pyx_v_b->core.qual > __pyx_v_q);
+ if (__pyx_t_2) {
+ __pyx_v_b->core.qual = __pyx_v_q;
+ goto __pyx_L10;
+ }
+ __pyx_L10:;
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1897
- * # so allocate 40 bytes for a new read
- * self._delegate.m_data = 40
- * self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 ) # <<<<<<<<<<<<<<
- * self._delegate.data_len = 0
+ /* "csamtools.pyx":1756
+ * if q < 0: skip = 1
+ * elif b.core.qual > q: b.core.qual = q
+ * if b.core.flag & BAM_FUNMAP: skip = 1 # <<<<<<<<<<<<<<
+ * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data = ((uint8_t *)calloc(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data, 1));
+ __pyx_t_7 = (__pyx_v_b->core.flag & 4);
+ if (__pyx_t_7) {
+ __pyx_v_skip = 1;
+ goto __pyx_L11;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1898
- * self._delegate.m_data = 40
- * self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
- * self._delegate.data_len = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1757
+ * elif b.core.qual > q: b.core.qual = q
+ * if b.core.flag & BAM_FUNMAP: skip = 1
+ * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 # <<<<<<<<<<<<<<
*
- * def __dealloc__(self):
+ * if not skip: break
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data_len = 0;
-
- __pyx_r = 0;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ if ((__pyx_v_b->core.flag & 1)) {
+ __pyx_t_2 = (!(__pyx_v_b->core.flag & 2));
+ __pyx_t_1 = __pyx_t_2;
+ } else {
+ __pyx_t_1 = (__pyx_v_b->core.flag & 1);
+ }
+ if (__pyx_t_1) {
+ __pyx_v_skip = 1;
+ goto __pyx_L11;
+ }
+ __pyx_L11:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1900
- * self._delegate.data_len = 0
+ /* "csamtools.pyx":1759
+ * elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * bam_destroy1(self._delegate)
+ * if not skip: break # <<<<<<<<<<<<<<
+ * # additional filters
*
*/
+ __pyx_t_1 = (!__pyx_v_skip);
+ if (__pyx_t_1) {
+ goto __pyx_L7_break;
+ goto __pyx_L12;
+ }
+ __pyx_L12:;
-static void __pyx_pf_9csamtools_11AlignedRead___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_11AlignedRead___dealloc__(PyObject *__pyx_v_self) {
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1900);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1901
+ /* "csamtools.pyx":1762
+ * # additional filters
*
- * def __dealloc__(self):
- * bam_destroy1(self._delegate) # <<<<<<<<<<<<<<
+ * ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
*
- * def __str__(self):
+ * return ret
+ */
+ __pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
+ }
+ __pyx_L7_break:;
+
+ /* "csamtools.pyx":1764
+ * ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
+ *
+ * return ret # <<<<<<<<<<<<<<
+ *
+ * cdef class IteratorColumn:
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate);
+ __pyx_r = __pyx_v_ret;
+ goto __pyx_L0;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_WriteUnraisable("csamtools.__advance_snpcalls", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
+ __pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1903
- * bam_destroy1(self._delegate)
- *
- * def __str__(self): # <<<<<<<<<<<<<<
- * """return string representation of alignment.
+/* Python wrapper */
+static int __pyx_pw_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ PyObject *__pyx_v_kwargs = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ {
+ PyObject* values[1] = {0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ }
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
+ __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_14IteratorColumn___cinit__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1813
+ * '''
*
+ * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead___str__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead___str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_11AlignedRead___str__;
-static PyObject *__pyx_pf_9csamtools_11AlignedRead___str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
+static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- PyObject *__pyx_t_12 = NULL;
- PyObject *__pyx_t_13 = NULL;
- PyObject *__pyx_t_14 = NULL;
+ int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 1903);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1915
- * # sam-parsing is done in sam.c/bam_format1_core which
- * # requires a valid header.
- * return "\t".join(map(str, (self.qname, # <<<<<<<<<<<<<<
- * self.flag,
- * self.rname,
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1813);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1916
- * # requires a valid header.
- * return "\t".join(map(str, (self.qname,
- * self.flag, # <<<<<<<<<<<<<<
- * self.rname,
- * self.pos,
+ /* "csamtools.pyx":1814
+ *
+ * def __cinit__( self, Samfile samfile, **kwargs ):
+ * self.samfile = samfile # <<<<<<<<<<<<<<
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ * self.fastafile = kwargs.get( "fastafile", None )
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1917
- * return "\t".join(map(str, (self.qname,
- * self.flag,
- * self.rname, # <<<<<<<<<<<<<<
- * self.pos,
- * self.mapq,
+ /* "csamtools.pyx":1815
+ * def __cinit__( self, Samfile samfile, **kwargs ):
+ * self.samfile = samfile
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK ) # <<<<<<<<<<<<<<
+ * self.fastafile = kwargs.get( "fastafile", None )
+ * self.stepper = kwargs.get( "stepper", None )
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__mask), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_self->mask = __pyx_t_3;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1918
- * self.flag,
- * self.rname,
- * self.pos, # <<<<<<<<<<<<<<
- * self.mapq,
- * self.cigar,
+ /* "csamtools.pyx":1816
+ * self.samfile = samfile
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ * self.fastafile = kwargs.get( "fastafile", None ) # <<<<<<<<<<<<<<
+ * self.stepper = kwargs.get( "stepper", None )
+ * self.max_depth = kwargs.get( "max_depth", 8000 )
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1918; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__fastafile), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_v_self->fastafile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
+ __pyx_v_self->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1919
- * self.rname,
- * self.pos,
- * self.mapq, # <<<<<<<<<<<<<<
- * self.cigar,
- * self.mrnm,
+ /* "csamtools.pyx":1817
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ * self.fastafile = kwargs.get( "fastafile", None )
+ * self.stepper = kwargs.get( "stepper", None ) # <<<<<<<<<<<<<<
+ * self.max_depth = kwargs.get( "max_depth", 8000 )
+ * self.iterdata.seq = NULL
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapq); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__stepper), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_v_self->stepper);
+ __Pyx_DECREF(__pyx_v_self->stepper);
+ __pyx_v_self->stepper = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1920
- * self.pos,
- * self.mapq,
- * self.cigar, # <<<<<<<<<<<<<<
- * self.mrnm,
- * self.mpos,
+ /* "csamtools.pyx":1818
+ * self.fastafile = kwargs.get( "fastafile", None )
+ * self.stepper = kwargs.get( "stepper", None )
+ * self.max_depth = kwargs.get( "max_depth", 8000 ) # <<<<<<<<<<<<<<
+ * self.iterdata.seq = NULL
+ * self.tid = 0
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__max_depth), __pyx_int_8000); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_self->max_depth = __pyx_t_3;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1921
- * self.mapq,
- * self.cigar,
- * self.mrnm, # <<<<<<<<<<<<<<
- * self.mpos,
- * self.rlen,
+ /* "csamtools.pyx":1819
+ * self.stepper = kwargs.get( "stepper", None )
+ * self.max_depth = kwargs.get( "max_depth", 8000 )
+ * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
+ * self.tid = 0
+ * self.pos = 0
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mrnm); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_v_self->iterdata.seq = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1922
- * self.cigar,
- * self.mrnm,
- * self.mpos, # <<<<<<<<<<<<<<
- * self.rlen,
- * self.seq,
+ /* "csamtools.pyx":1820
+ * self.max_depth = kwargs.get( "max_depth", 8000 )
+ * self.iterdata.seq = NULL
+ * self.tid = 0 # <<<<<<<<<<<<<<
+ * self.pos = 0
+ * self.n_plp = 0
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mpos); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_v_self->tid = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1923
- * self.mrnm,
- * self.mpos,
- * self.rlen, # <<<<<<<<<<<<<<
- * self.seq,
- * self.qual,
+ /* "csamtools.pyx":1821
+ * self.iterdata.seq = NULL
+ * self.tid = 0
+ * self.pos = 0 # <<<<<<<<<<<<<<
+ * self.n_plp = 0
+ * self.plp = NULL
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rlen); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_v_self->pos = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1924
- * self.mpos,
- * self.rlen,
- * self.seq, # <<<<<<<<<<<<<<
- * self.qual,
- * self.tags )))
+ /* "csamtools.pyx":1822
+ * self.tid = 0
+ * self.pos = 0
+ * self.n_plp = 0 # <<<<<<<<<<<<<<
+ * self.plp = NULL
+ * self.pileup_iter = <bam_plp_t>NULL
*/
- __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_v_self->n_plp = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1925
- * self.rlen,
- * self.seq,
- * self.qual, # <<<<<<<<<<<<<<
- * self.tags )))
+ /* "csamtools.pyx":1823
+ * self.pos = 0
+ * self.n_plp = 0
+ * self.plp = NULL # <<<<<<<<<<<<<<
+ * self.pileup_iter = <bam_plp_t>NULL
*
*/
- __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __pyx_v_self->plp = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1926
- * self.seq,
- * self.qual,
- * self.tags ))) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1824
+ * self.n_plp = 0
+ * self.plp = NULL
+ * self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
+ *
*
- * def compare(self, AlignedRead other):
*/
- __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tags); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_14 = PyTuple_New(12); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_14, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_14, 3, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_14, 4, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_14, 5, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_14, 6, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_14, 7, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_14, 8, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_14, 9, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
- PyTuple_SET_ITEM(__pyx_t_14, 10, __pyx_t_12);
- __Pyx_GIVEREF(__pyx_t_12);
- PyTuple_SET_ITEM(__pyx_t_14, 11, __pyx_t_13);
- __Pyx_GIVEREF(__pyx_t_13);
- __pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_7 = 0;
- __pyx_t_8 = 0;
- __pyx_t_9 = 0;
- __pyx_t_10 = 0;
- __pyx_t_11 = 0;
- __pyx_t_12 = 0;
- __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(2); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_builtin_map, __pyx_t_13, NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_1, __pyx_t_13, NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_r = __pyx_t_14;
- __pyx_t_14 = 0;
- goto __pyx_L0;
+ __pyx_v_self->pileup_iter = NULL;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_XDECREF(__pyx_t_12);
- __Pyx_XDECREF(__pyx_t_13);
- __Pyx_XDECREF(__pyx_t_14);
- __Pyx_AddTraceback("csamtools.AlignedRead.__str__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1928
- * self.tags )))
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_2__iter__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1827
*
- * def compare(self, AlignedRead other): # <<<<<<<<<<<<<<
- * '''return -1,0,1, if contents in this are binary <,=,> to *other*'''
+ *
+ * def __iter__(self): # <<<<<<<<<<<<<<
+ * return self
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
- int __pyx_v_retval;
- bam1_t *__pyx_v_t;
- bam1_t *__pyx_v_o;
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("compare");
- __Pyx_TraceCall("compare", __pyx_f[0], 1928);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1827);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1934
- * cdef bam1_t *t, *o
+ /* "csamtools.pyx":1828
*
- * t = self._delegate # <<<<<<<<<<<<<<
- * o = other._delegate
+ * def __iter__(self):
+ * return self # <<<<<<<<<<<<<<
*
+ * cdef int cnext(self):
*/
- __pyx_v_t = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1935
- *
- * t = self._delegate
- * o = other._delegate # <<<<<<<<<<<<<<
- *
- * # uncomment for debugging purposes
- */
- __pyx_v_o = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other)->_delegate;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1947
+/* "csamtools.pyx":1830
+ * return self
*
- * # Fast-path test for object identity
- * if t==o: # <<<<<<<<<<<<<<
- * return 0
+ * cdef int cnext(self): # <<<<<<<<<<<<<<
+ * '''perform next iteration.
*
*/
- __pyx_t_1 = (__pyx_v_t == __pyx_v_o);
- if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1948
- * # Fast-path test for object identity
- * if t==o:
- * return 0 # <<<<<<<<<<<<<<
- *
- * retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_int_0);
- __pyx_r = __pyx_int_0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1830);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1950
- * return 0
- *
- * retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t)) # <<<<<<<<<<<<<<
- *
- * if retval: return retval
+ /* "csamtools.pyx":1836
+ * It has been re-implemented to permit for filtering.
+ * '''
+ * self.plp = bam_plp_auto( self.pileup_iter, # <<<<<<<<<<<<<<
+ * &self.tid,
+ * &self.pos,
*/
- __pyx_v_retval = memcmp((&__pyx_v_t->core), (&__pyx_v_o->core), (sizeof(bam1_core_t)));
+ __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1952
- * retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
- *
- * if retval: return retval # <<<<<<<<<<<<<<
- * retval = cmp(t.data_len, o.data_len)
- * if retval: return retval
- */
- if (__pyx_v_retval) {
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1952; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_r = 0;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1953
+/* "csamtools.pyx":1841
+ * &self.n_plp )
*
- * if retval: return retval
- * retval = cmp(t.data_len, o.data_len) # <<<<<<<<<<<<<<
- * if retval: return retval
- * return memcmp(t.data, o.data, t.data_len)
+ * cdef char * getSequence( self ): # <<<<<<<<<<<<<<
+ * '''return current reference sequence underlying the iterator.
+ * '''
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_t->data_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_o->data_len); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_cmp, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_retval = __pyx_t_5;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1954
- * if retval: return retval
- * retval = cmp(t.data_len, o.data_len)
- * if retval: return retval # <<<<<<<<<<<<<<
- * return memcmp(t.data, o.data, t.data_len)
+static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+ char *__pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("getSequence", 0);
+ __Pyx_TraceCall("getSequence", __pyx_f[0], 1841);
+
+ /* "csamtools.pyx":1844
+ * '''return current reference sequence underlying the iterator.
+ * '''
+ * return self.iterdata.seq # <<<<<<<<<<<<<<
*
+ * property seq_len:
*/
- if (__pyx_v_retval) {
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
- goto __pyx_L7;
- }
- __pyx_L7:;
+ __pyx_r = __pyx_v_self->iterdata.seq;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1955
- * retval = cmp(t.data_len, o.data_len)
- * if retval: return retval
- * return memcmp(t.data, o.data, t.data_len) # <<<<<<<<<<<<<<
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1848
+ * property seq_len:
+ * '''current sequence length.'''
+ * def __get__(self): return self.iterdata.seq_len # <<<<<<<<<<<<<<
*
- * # Disabled so long as __cmp__ is a special method
+ * def addReference( self, Fastafile fastafile ):
*/
+
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1848);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(memcmp(__pyx_v_t->data, __pyx_v_o->data, __pyx_v_t->data_len)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.AlignedRead.compare");
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.seq_len.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1958
- *
- * # Disabled so long as __cmp__ is a special method
- * def __hash__(self): # <<<<<<<<<<<<<<
- * return _Py_HashPointer(<void *>self)
- *
- */
-
-static long __pyx_pf_9csamtools_11AlignedRead___hash__(PyObject *__pyx_v_self); /*proto*/
-static long __pyx_pf_9csamtools_11AlignedRead___hash__(PyObject *__pyx_v_self) {
- long __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__hash__");
- __Pyx_TraceCall("__hash__", __pyx_f[0], 1958);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1959
- * # Disabled so long as __cmp__ is a special method
- * def __hash__(self):
- * return _Py_HashPointer(<void *>self) # <<<<<<<<<<<<<<
- *
- * property qname:
- */
- __pyx_r = _Py_HashPointer(((void *)__pyx_v_self));
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorColumn_4addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("addReference (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_4addReference(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_fastafile));
goto __pyx_L0;
-
- __pyx_r = 0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
__pyx_L0:;
- if (unlikely(__pyx_r == -1) && !PyErr_Occurred()) __pyx_r = -2;
- __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1963
- * property qname:
- * """the query name (None if not present)"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * src = self._delegate
+/* "csamtools.pyx":1850
+ * def __get__(self): return self.iterdata.seq_len
+ *
+ * def addReference( self, Fastafile fastafile ): # <<<<<<<<<<<<<<
+ * '''
+ * add reference sequences in *fastafile* to iterator.'''
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Fastafile *__pyx_v_fastafile) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1963);
+ __Pyx_RefNannySetupContext("addReference", 0);
+ __Pyx_TraceCall("addReference", __pyx_f[0], 1850);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1965
- * def __get__(self):
- * cdef bam1_t * src
- * src = self._delegate # <<<<<<<<<<<<<<
- * if src.core.l_qname == 0: return None
- * return <char *>bam1_qname( src )
+ /* "csamtools.pyx":1853
+ * '''
+ * add reference sequences in *fastafile* to iterator.'''
+ * self.fastafile = fastafile # <<<<<<<<<<<<<<
+ * if self.iterdata.seq != NULL: free(self.iterdata.seq)
+ * self.iterdata.tid = -1
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __Pyx_INCREF(((PyObject *)__pyx_v_fastafile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_fastafile));
+ __Pyx_GOTREF(__pyx_v_self->fastafile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
+ __pyx_v_self->fastafile = __pyx_v_fastafile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1966
- * cdef bam1_t * src
- * src = self._delegate
- * if src.core.l_qname == 0: return None # <<<<<<<<<<<<<<
- * return <char *>bam1_qname( src )
- *
+ /* "csamtools.pyx":1854
+ * add reference sequences in *fastafile* to iterator.'''
+ * self.fastafile = fastafile
+ * if self.iterdata.seq != NULL: free(self.iterdata.seq) # <<<<<<<<<<<<<<
+ * self.iterdata.tid = -1
+ * self.iterdata.fastafile = self.fastafile.fastafile
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qname == 0);
+ __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
+ free(__pyx_v_self->iterdata.seq);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1967
- * src = self._delegate
- * if src.core.l_qname == 0: return None
- * return <char *>bam1_qname( src ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1855
+ * self.fastafile = fastafile
+ * if self.iterdata.seq != NULL: free(self.iterdata.seq)
+ * self.iterdata.tid = -1 # <<<<<<<<<<<<<<
+ * self.iterdata.fastafile = self.fastafile.fastafile
*
- * def __set__(self, qname ):
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(bam1_qname(__pyx_v_src)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
- goto __pyx_L0;
+ __pyx_v_self->iterdata.tid = -1;
+
+ /* "csamtools.pyx":1856
+ * if self.iterdata.seq != NULL: free(self.iterdata.seq)
+ * self.iterdata.tid = -1
+ * self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
+ *
+ * def hasReference( self ):
+ */
+ __pyx_v_self->iterdata.fastafile = __pyx_v_self->fastafile->fastafile;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qname.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1969
- * return <char *>bam1_qname( src )
- *
- * def __set__(self, qname ): # <<<<<<<<<<<<<<
- * if qname == None or len(qname) == 0: return
- * cdef bam1_t * src
- */
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorColumn_6hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
+static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("hasReference (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_6hasReference(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
-static int __pyx_pf_9csamtools_11AlignedRead_5qname___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5qname___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
- bam1_t *__pyx_v_src;
- int __pyx_v_l;
- char *__pyx_v_p;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- Py_ssize_t __pyx_t_3;
- int __pyx_t_4;
- int __pyx_t_5;
- char *__pyx_t_6;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 1969);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1970
- *
- * def __set__(self, qname ):
- * if qname == None or len(qname) == 0: return # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * cdef int l
- */
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = (__pyx_t_3 == 0);
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_2;
- }
- if (__pyx_t_5) {
- __pyx_r = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1975
- * cdef char * p
- *
- * src = self._delegate # <<<<<<<<<<<<<<
- * p = bam1_qname( src )
+/* "csamtools.pyx":1858
+ * self.iterdata.fastafile = self.fastafile.fastafile
*
+ * def hasReference( self ): # <<<<<<<<<<<<<<
+ * '''
+ * return true if iterator is associated with a reference'''
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1976
- *
- * src = self._delegate
- * p = bam1_qname( src ) # <<<<<<<<<<<<<<
- *
- * # the qname is \0 terminated
- */
- __pyx_v_p = bam1_qname(__pyx_v_src);
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("hasReference", 0);
+ __Pyx_TraceCall("hasReference", __pyx_f[0], 1858);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1979
+ /* "csamtools.pyx":1861
+ * '''
+ * return true if iterator is associated with a reference'''
+ * return self.fastafile # <<<<<<<<<<<<<<
*
- * # the qname is \0 terminated
- * l = len(qname) + 1 # <<<<<<<<<<<<<<
- * pysam_bam_update( src,
- * src.core.l_qname,
+ * cdef setMask( self, mask ):
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_l = (__pyx_t_3 + 1);
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->fastafile));
+ __pyx_r = ((PyObject *)__pyx_v_self->fastafile);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1983
- * src.core.l_qname,
- * l,
- * <uint8_t*>p ) # <<<<<<<<<<<<<<
- *
- * src.core.l_qname = l
- */
- pysam_bam_update(__pyx_v_src, __pyx_v_src->core.l_qname, __pyx_v_l, ((uint8_t *)__pyx_v_p));
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1985
- * <uint8_t*>p )
+/* "csamtools.pyx":1863
+ * return self.fastafile
*
- * src.core.l_qname = l # <<<<<<<<<<<<<<
+ * cdef setMask( self, mask ): # <<<<<<<<<<<<<<
+ * '''set masking flag in iterator.
*
- * # re-acquire pointer to location in memory
*/
- __pyx_v_src->core.l_qname = __pyx_v_l;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1989
- * # re-acquire pointer to location in memory
- * # as it might have moved
- * p = bam1_qname(src) # <<<<<<<<<<<<<<
+static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_mask) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setMask", 0);
+ __Pyx_TraceCall("setMask", __pyx_f[0], 1863);
+
+ /* "csamtools.pyx":1868
+ * reads with bits set in *mask* will be skipped.
+ * '''
+ * self.mask = mask # <<<<<<<<<<<<<<
+ * bam_plp_set_mask( self.pileup_iter, self.mask )
*
- * strncpy( p, qname, l )
*/
- __pyx_v_p = bam1_qname(__pyx_v_src);
+ __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_mask); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->mask = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1991
- * p = bam1_qname(src)
- *
- * strncpy( p, qname, l ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1869
+ * '''
+ * self.mask = mask
+ * bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
*
- * property cigar:
+ * cdef setupIteratorData( self,
*/
- __pyx_t_6 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy(__pyx_v_p, __pyx_t_6, __pyx_v_l);
+ bam_plp_set_mask(__pyx_v_self->pileup_iter, __pyx_v_self->mask);
- __pyx_r = 0;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.qname.__set__");
- __pyx_r = -1;
+ __Pyx_AddTraceback("csamtools.IteratorColumn.setMask", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1996
- * """the :term:`cigar` alignment (None if not present).
- * """
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef uint32_t * cigar_p
- * cdef bam1_t * src
+/* "csamtools.pyx":1871
+ * bam_plp_set_mask( self.pileup_iter, self.mask )
+ *
+ * cdef setupIteratorData( self, # <<<<<<<<<<<<<<
+ * int tid,
+ * int start,
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self) {
- uint32_t *__pyx_v_cigar_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_op;
- PyObject *__pyx_v_l;
- PyObject *__pyx_v_cigar;
- int __pyx_v_k;
+static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args) {
+ int __pyx_v_reopen = ((int)0);
PyObject *__pyx_r = NULL;
- int __pyx_t_1;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- uint32_t __pyx_t_3;
+ PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ int __pyx_t_6;
+ int __pyx_t_7;
+ int __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1996);
- __pyx_v_op = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_l = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_cigar = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2002
- * cdef int k
- *
- * src = self._delegate # <<<<<<<<<<<<<<
- * if src.core.n_cigar == 0: return None
- *
- */
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2003
- *
- * src = self._delegate
- * if src.core.n_cigar == 0: return None # <<<<<<<<<<<<<<
- *
- * cigar = []
- */
- __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
+ __Pyx_RefNannySetupContext("setupIteratorData", 0);
+ __Pyx_TraceCall("setupIteratorData", __pyx_f[0], 1871);
+ if (__pyx_optional_args) {
+ if (__pyx_optional_args->__pyx_n > 0) {
+ __pyx_v_reopen = __pyx_optional_args->reopen;
+ }
}
- __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2005
- * if src.core.n_cigar == 0: return None
+ /* "csamtools.pyx":1878
+ * '''setup the iterator structure'''
*
- * cigar = [] # <<<<<<<<<<<<<<
- * cigar_p = bam1_cigar(src);
- * for k from 0 <= k < src.core.n_cigar:
+ * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen ) # <<<<<<<<<<<<<<
+ * self.iterdata.samfile = self.samfile.samfile
+ * self.iterdata.iter = self.iter.iter
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(__pyx_v_cigar);
- __pyx_v_cigar = ((PyObject *)__pyx_t_2);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_1 = 0;
__pyx_t_2 = 0;
+ __pyx_t_3 = 0;
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_v_self->iter);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
+ __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2006
+ /* "csamtools.pyx":1879
*
- * cigar = []
- * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
+ * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
+ * self.iterdata.samfile = self.samfile.samfile # <<<<<<<<<<<<<<
+ * self.iterdata.iter = self.iter.iter
+ * self.iterdata.seq = NULL
*/
- __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
+ __pyx_v_self->iterdata.samfile = __pyx_v_self->samfile->samfile;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2007
- * cigar = []
- * cigar_p = bam1_cigar(src);
- * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ /* "csamtools.pyx":1880
+ * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
+ * self.iterdata.samfile = self.samfile.samfile
+ * self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
+ * self.iterdata.seq = NULL
+ * self.iterdata.tid = -1
*/
- __pyx_t_3 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
+ __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2008
- * cigar_p = bam1_cigar(src);
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- * cigar.append((op, l))
+ /* "csamtools.pyx":1881
+ * self.iterdata.samfile = self.samfile.samfile
+ * self.iterdata.iter = self.iter.iter
+ * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
+ * self.iterdata.tid = -1
+ *
*/
- __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_self->iterdata.seq = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2009
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
- * cigar.append((op, l))
- * return cigar
+ /* "csamtools.pyx":1882
+ * self.iterdata.iter = self.iter.iter
+ * self.iterdata.seq = NULL
+ * self.iterdata.tid = -1 # <<<<<<<<<<<<<<
+ *
+ * if self.fastafile != None:
*/
- __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_self->iterdata.tid = -1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2010
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- * cigar.append((op, l)) # <<<<<<<<<<<<<<
- * return cigar
+ /* "csamtools.pyx":1884
+ * self.iterdata.tid = -1
*
+ * if self.fastafile != None: # <<<<<<<<<<<<<<
+ * self.iterdata.fastafile = self.fastafile.fastafile
+ * else:
*/
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2010; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_op);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op);
- __Pyx_GIVEREF(__pyx_v_op);
- __Pyx_INCREF(__pyx_v_l);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_l);
- __Pyx_GIVEREF(__pyx_v_l);
- __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_cigar, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2010; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_self->fastafile), Py_None, Py_NE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ if (__pyx_t_6) {
+
+ /* "csamtools.pyx":1885
+ *
+ * if self.fastafile != None:
+ * self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
+ * else:
+ * self.iterdata.fastafile = NULL
+ */
+ __pyx_v_self->iterdata.fastafile = __pyx_v_self->fastafile->fastafile;
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":1887
+ * self.iterdata.fastafile = self.fastafile.fastafile
+ * else:
+ * self.iterdata.fastafile = NULL # <<<<<<<<<<<<<<
+ *
+ * if self.stepper == None or self.stepper == "all":
+ */
+ __pyx_v_self->iterdata.fastafile = NULL;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":1889
+ * self.iterdata.fastafile = NULL
+ *
+ * if self.stepper == None or self.stepper == "all": # <<<<<<<<<<<<<<
+ * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
+ * elif self.stepper == "samtools":
+ */
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, Py_None, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ if (!__pyx_t_6) {
+ __pyx_t_7 = __Pyx_PyString_Equals(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __pyx_t_7;
+ } else {
+ __pyx_t_8 = __pyx_t_6;
+ }
+ if (__pyx_t_8) {
+
+ /* "csamtools.pyx":1890
+ *
+ * if self.stepper == None or self.stepper == "all":
+ * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata ) # <<<<<<<<<<<<<<
+ * elif self.stepper == "samtools":
+ * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
+ */
+ __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_all), (&__pyx_v_self->iterdata));
+ goto __pyx_L4;
+ }
+
+ /* "csamtools.pyx":1891
+ * if self.stepper == None or self.stepper == "all":
+ * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
+ * elif self.stepper == "samtools": # <<<<<<<<<<<<<<
+ * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
+ * else:
+ */
+ __pyx_t_8 = __Pyx_PyString_Equals(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__samtools), Py_EQ); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_8) {
+
+ /* "csamtools.pyx":1892
+ * self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
+ * elif self.stepper == "samtools":
+ * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata ) # <<<<<<<<<<<<<<
+ * else:
+ * raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
+ */
+ __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_snpcalls), (&__pyx_v_self->iterdata));
+ goto __pyx_L4;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":1894
+ * self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
+ * else:
+ * raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) # <<<<<<<<<<<<<<
+ *
+ * if self.max_depth:
+ */
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_127), __pyx_v_self->stepper); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2011
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- * cigar.append((op, l))
- * return cigar # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1896
+ * raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
+ *
+ * if self.max_depth: # <<<<<<<<<<<<<<
+ * bam_plp_set_maxcnt( self.pileup_iter, self.max_depth )
*
- * def __set__(self, values ):
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_cigar);
- __pyx_r = __pyx_v_cigar;
- goto __pyx_L0;
+ if (__pyx_v_self->max_depth) {
+
+ /* "csamtools.pyx":1897
+ *
+ * if self.max_depth:
+ * bam_plp_set_maxcnt( self.pileup_iter, self.max_depth ) # <<<<<<<<<<<<<<
+ *
+ * bam_plp_set_mask( self.pileup_iter, self.mask )
+ */
+ bam_plp_set_maxcnt(__pyx_v_self->pileup_iter, __pyx_v_self->max_depth);
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
+
+ /* "csamtools.pyx":1899
+ * bam_plp_set_maxcnt( self.pileup_iter, self.max_depth )
+ *
+ * bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
+ *
+ * cdef reset( self, tid, start, end ):
+ */
+ bam_plp_set_mask(__pyx_v_self->pileup_iter, __pyx_v_self->mask);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__get__");
- __pyx_r = NULL;
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.setupIteratorData", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_op);
- __Pyx_DECREF(__pyx_v_l);
- __Pyx_DECREF(__pyx_v_cigar);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2013
- * return cigar
+/* "csamtools.pyx":1901
+ * bam_plp_set_mask( self.pileup_iter, self.mask )
+ *
+ * cdef reset( self, tid, start, end ): # <<<<<<<<<<<<<<
+ * '''reset iterator position.
*
- * def __set__(self, values ): # <<<<<<<<<<<<<<
- * if values == None or len(values) == 0: return
- * cdef uint32_t * p
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
- uint32_t *__pyx_v_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_op;
- PyObject *__pyx_v_l;
- int __pyx_v_k;
- int __pyx_r;
+static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_end) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- Py_ssize_t __pyx_t_3;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_t_4;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- uint32_t __pyx_t_10;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2013);
- __pyx_v_op = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_l = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_TraceCall("reset", __pyx_f[0], 1901);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2014
+ /* "csamtools.pyx":1907
+ * having to incur the full set-up costs.
+ * '''
+ * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 ) # <<<<<<<<<<<<<<
+ * self.iterdata.iter = self.iter.iter
*
- * def __set__(self, values ):
- * if values == None or len(values) == 0: return # <<<<<<<<<<<<<<
- * cdef uint32_t * p
- * cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = (__pyx_t_3 == 0);
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_2;
- }
- if (__pyx_t_5) {
- __pyx_r = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ __Pyx_INCREF(__pyx_v_tid);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_tid);
+ __Pyx_GIVEREF(__pyx_v_tid);
+ __Pyx_INCREF(__pyx_v_start);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_start);
+ __Pyx_GIVEREF(__pyx_v_start);
+ __Pyx_INCREF(__pyx_v_end);
+ PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_end);
+ __Pyx_GIVEREF(__pyx_v_end);
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_v_self->iter);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
+ __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2020
- * cdef int k
- *
- * k = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1908
+ * '''
+ * self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 )
+ * self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
*
- * src = self._delegate
+ * # invalidate sequence if different tid
*/
- __pyx_v_k = 0;
+ __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2022
- * k = 0
- *
- * src = self._delegate # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1911
*
- * # get location of cigar string
+ * # invalidate sequence if different tid
+ * if self.tid != tid: # <<<<<<<<<<<<<<
+ * if self.iterdata.seq != NULL: free( self.iterdata.seq )
+ * self.iterdata.seq = NULL
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_v_tid, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2025
- *
- * # get location of cigar string
- * p = bam1_cigar(src) # <<<<<<<<<<<<<<
- *
- * # create space for cigar data within src.data
+ /* "csamtools.pyx":1912
+ * # invalidate sequence if different tid
+ * if self.tid != tid:
+ * if self.iterdata.seq != NULL: free( self.iterdata.seq ) # <<<<<<<<<<<<<<
+ * self.iterdata.seq = NULL
+ * self.iterdata.tid = -1
*/
- __pyx_v_p = bam1_cigar(__pyx_v_src);
+ __pyx_t_4 = (__pyx_v_self->iterdata.seq != NULL);
+ if (__pyx_t_4) {
+ free(__pyx_v_self->iterdata.seq);
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2030
- * pysam_bam_update( src,
- * src.core.n_cigar * 4,
- * len(values) * 4, # <<<<<<<<<<<<<<
- * <uint8_t*>p )
+ /* "csamtools.pyx":1913
+ * if self.tid != tid:
+ * if self.iterdata.seq != NULL: free( self.iterdata.seq )
+ * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
+ * self.iterdata.tid = -1
*
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->iterdata.seq = NULL;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2031
- * src.core.n_cigar * 4,
- * len(values) * 4,
- * <uint8_t*>p ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1914
+ * if self.iterdata.seq != NULL: free( self.iterdata.seq )
+ * self.iterdata.seq = NULL
+ * self.iterdata.tid = -1 # <<<<<<<<<<<<<<
*
- * # length is number of cigar operations, not bytes
+ * # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata )
*/
- pysam_bam_update(__pyx_v_src, (__pyx_v_src->core.n_cigar * 4), (__pyx_t_3 * 4), ((uint8_t *)__pyx_v_p));
+ __pyx_v_self->iterdata.tid = -1;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2034
+ /* "csamtools.pyx":1917
*
- * # length is number of cigar operations, not bytes
- * src.core.n_cigar = len(values) # <<<<<<<<<<<<<<
+ * # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata )
+ * bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
*
- * # re-acquire pointer to location in memory
+ * def __dealloc__(self):
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_src->core.n_cigar = __pyx_t_3;
+ bam_plp_reset(__pyx_v_self->pileup_iter);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2038
- * # re-acquire pointer to location in memory
- * # as it might have moved
- * p = bam1_cigar(src) # <<<<<<<<<<<<<<
- *
- * # insert cigar operations
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static void __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "csamtools.pyx":1919
+ * bam_plp_reset(self.pileup_iter)
+ *
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * # reset in order to avoid memory leak messages for iterators that have
+ * # not been fully consumed
*/
- __pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2041
+static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1919);
+
+ /* "csamtools.pyx":1922
+ * # reset in order to avoid memory leak messages for iterators that have
+ * # not been fully consumed
+ * if self.pileup_iter != <bam_plp_t>NULL: # <<<<<<<<<<<<<<
+ * bam_plp_reset(self.pileup_iter)
+ * bam_plp_destroy(self.pileup_iter)
+ */
+ __pyx_t_1 = (__pyx_v_self->pileup_iter != NULL);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":1923
+ * # not been fully consumed
+ * if self.pileup_iter != <bam_plp_t>NULL:
+ * bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
+ * bam_plp_destroy(self.pileup_iter)
+ * self.pileup_iter = <bam_plp_t>NULL
+ */
+ bam_plp_reset(__pyx_v_self->pileup_iter);
+
+ /* "csamtools.pyx":1924
+ * if self.pileup_iter != <bam_plp_t>NULL:
+ * bam_plp_reset(self.pileup_iter)
+ * bam_plp_destroy(self.pileup_iter) # <<<<<<<<<<<<<<
+ * self.pileup_iter = <bam_plp_t>NULL
*
- * # insert cigar operations
- * for op, l in values: # <<<<<<<<<<<<<<
- * p[k] = l << BAM_CIGAR_SHIFT | op
- * k += 1
*/
- if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
- __pyx_t_3 = 0; __pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1);
- } else {
- __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ bam_plp_destroy(__pyx_v_self->pileup_iter);
+
+ /* "csamtools.pyx":1925
+ * bam_plp_reset(self.pileup_iter)
+ * bam_plp_destroy(self.pileup_iter)
+ * self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
+ *
+ * if self.iterdata.seq != NULL:
+ */
+ __pyx_v_self->pileup_iter = NULL;
+ goto __pyx_L3;
}
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_1))) {
- if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_1))) {
- if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ __pyx_L3:;
+
+ /* "csamtools.pyx":1927
+ * self.pileup_iter = <bam_plp_t>NULL
+ *
+ * if self.iterdata.seq != NULL: # <<<<<<<<<<<<<<
+ * free(self.iterdata.seq)
+ * self.iterdata.seq = NULL
+ */
+ __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":1928
+ *
+ * if self.iterdata.seq != NULL:
+ * free(self.iterdata.seq) # <<<<<<<<<<<<<<
+ * self.iterdata.seq = NULL
+ *
+ */
+ free(__pyx_v_self->iterdata.seq);
+
+ /* "csamtools.pyx":1929
+ * if self.iterdata.seq != NULL:
+ * free(self.iterdata.seq)
+ * self.iterdata.seq = NULL # <<<<<<<<<<<<<<
+ *
+ * cdef class IteratorColumnRegion(IteratorColumn):
+ */
+ __pyx_v_self->iterdata.seq = NULL;
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+}
+
+/* Python wrapper */
+static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ int __pyx_v_tid;
+ int __pyx_v_start;
+ int __pyx_v_end;
+ int __pyx_v_truncate;
+ CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ {
+ PyObject* values[5] = {0,0,0,0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ case 3:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (value) { values[3] = value; kw_args--; }
+ }
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__truncate);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ if (values[1]) {
+ } else {
+ __pyx_v_tid = ((int)0);
+ }
+ if (values[2]) {
+ } else {
+ __pyx_v_start = ((int)0);
+ }
+ if (values[3]) {
+ } else {
+ __pyx_v_end = __pyx_k_128;
+ }
+ if (values[4]) {
+ } else {
+
+ /* "csamtools.pyx":1938
+ * int start = 0,
+ * int end = max_pos,
+ * int truncate = False, # <<<<<<<<<<<<<<
+ * **kwargs ):
+ *
+ */
+ __pyx_v_truncate = ((int)0);
+ }
} else {
- __pyx_t_6 = PyIter_Next(__pyx_t_1);
- if (!__pyx_t_6) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
break;
+ default: goto __pyx_L5_argtuple_error;
}
- __Pyx_GOTREF(__pyx_t_6);
}
- if (PyTuple_CheckExact(__pyx_t_6) && likely(PyTuple_GET_SIZE(__pyx_t_6) == 2)) {
- PyObject* tuple = __pyx_t_6;
- __pyx_t_7 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_7;
- __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ if (values[1]) {
+ __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1935; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
- __pyx_t_9 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __Pyx_UnpackItem(__pyx_t_9, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_UnpackItem(__pyx_t_9, 1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- if (__Pyx_EndUnpack(__pyx_t_9, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_7;
- __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_tid = ((int)0);
+ }
+ if (values[2]) {
+ __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1936; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_start = ((int)0);
+ }
+ if (values[3]) {
+ __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_end = __pyx_k_128;
}
+ if (values[4]) {
+ __pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_truncate = ((int)0);
+ }
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
+ __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_truncate, __pyx_v_kwargs);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2042
- * # insert cigar operations
- * for op, l in values:
- * p[k] = l << BAM_CIGAR_SHIFT | op # <<<<<<<<<<<<<<
- * k += 1
- *
+/* "csamtools.pyx":1934
+ * '''iterates over a region only.
+ * '''
+ * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
+ * int tid = 0,
+ * int start = 0,
*/
- __pyx_t_6 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyNumber_Or(__pyx_t_6, __pyx_v_op); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_10 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_10 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- (__pyx_v_p[__pyx_v_k]) = __pyx_t_10;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2043
- * for op, l in values:
- * p[k] = l << BAM_CIGAR_SHIFT | op
- * k += 1 # <<<<<<<<<<<<<<
+static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1934);
+
+ /* "csamtools.pyx":1942
*
- * ## setting the cigar string also updates the "bin" attribute
+ * # initialize iterator
+ * self.setupIteratorData( tid, start, end, 1 ) # <<<<<<<<<<<<<<
+ * self.start = start
+ * self.end = end
*/
- __pyx_v_k += 1;
- }
+ __pyx_t_2.__pyx_n = 1;
+ __pyx_t_2.reopen = 1;
+ __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2046
+ /* "csamtools.pyx":1943
+ * # initialize iterator
+ * self.setupIteratorData( tid, start, end, 1 )
+ * self.start = start # <<<<<<<<<<<<<<
+ * self.end = end
+ * self.truncate = truncate
+ */
+ __pyx_v_self->start = __pyx_v_start;
+
+ /* "csamtools.pyx":1944
+ * self.setupIteratorData( tid, start, end, 1 )
+ * self.start = start
+ * self.end = end # <<<<<<<<<<<<<<
+ * self.truncate = truncate
*
- * ## setting the cigar string also updates the "bin" attribute
- * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, p)) # <<<<<<<<<<<<<<
+ */
+ __pyx_v_self->end = __pyx_v_end;
+
+ /* "csamtools.pyx":1945
+ * self.start = start
+ * self.end = end
+ * self.truncate = truncate # <<<<<<<<<<<<<<
*
- * property seq:
+ * def __next__(self):
*/
- __pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), __pyx_v_p));
+ __pyx_v_self->truncate = __pyx_v_truncate;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__set__");
+ __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_op);
- __Pyx_DECREF(__pyx_v_l);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2050
- * property seq:
- * """read sequence bases, including :term:`soft clipped` bases (None if not present)"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * cdef char * s
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_20IteratorColumnRegion_2__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__;
+static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":1947
+ * self.truncate = truncate
+ *
+ * def __next__(self): # <<<<<<<<<<<<<<
+ * """python version of next().
+ * """
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
+static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2050);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1947);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2053
- * cdef bam1_t * src
- * cdef char * s
- * src = self._delegate # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1951
+ * """
*
- * if src.core.l_qseq == 0: return None
+ * while 1: # <<<<<<<<<<<<<<
+ * self.cnext()
+ * if self.n_plp < 0:
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ while (1) {
+ if (!1) break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2055
- * src = self._delegate
- *
- * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1952
*
- * return get_seq_range(src, 0, src.core.l_qseq)
+ * while 1:
+ * self.cnext() # <<<<<<<<<<<<<<
+ * if self.n_plp < 0:
+ * raise ValueError("error during iteration" )
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2057
- * if src.core.l_qseq == 0: return None
+ /* "csamtools.pyx":1953
+ * while 1:
+ * self.cnext()
+ * if self.n_plp < 0: # <<<<<<<<<<<<<<
+ * raise ValueError("error during iteration" )
*
- * return get_seq_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
- *
- * def __set__(self,seq):
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.seq.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2059
- * return get_seq_range(src, 0, src.core.l_qseq)
- *
- * def __set__(self,seq): # <<<<<<<<<<<<<<
- * # samtools manages sequence and quality length memory together
- * # if no quality information is present, the first byte says 0xff.
*/
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
+ if (__pyx_t_1) {
-static int __pyx_pf_9csamtools_11AlignedRead_3seq___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3seq___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
- bam1_t *__pyx_v_src;
- uint8_t *__pyx_v_p;
- char *__pyx_v_s;
- int __pyx_v_l;
- int __pyx_v_k;
- int __pyx_v_nbytes_new;
- int __pyx_v_nbytes_old;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- Py_ssize_t __pyx_t_3;
- int __pyx_t_4;
- int __pyx_t_5;
- int __pyx_t_6;
- char *__pyx_t_7;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2059);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2063
- * # if no quality information is present, the first byte says 0xff.
+ /* "csamtools.pyx":1954
+ * self.cnext()
+ * if self.n_plp < 0:
+ * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
*
- * if seq == None or len(seq) == 0: return # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * cdef uint8_t * p
+ * if self.plp == NULL:
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = (__pyx_t_3 == 0);
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_2;
- }
- if (__pyx_t_5) {
- __pyx_r = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_130), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2069
- * cdef int l, k, nbytes_new, nbytes_old
+ /* "csamtools.pyx":1956
+ * raise ValueError("error during iteration" )
*
- * src = self._delegate # <<<<<<<<<<<<<<
+ * if self.plp == NULL: # <<<<<<<<<<<<<<
+ * raise StopIteration
*
- * l = len(seq)
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.plp == NULL);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2071
- * src = self._delegate
+ /* "csamtools.pyx":1957
*
- * l = len(seq) # <<<<<<<<<<<<<<
+ * if self.plp == NULL:
+ * raise StopIteration # <<<<<<<<<<<<<<
*
- * # as the sequence is stored in half-bytes, the total length (sequence
+ * if self.truncate:
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_l = __pyx_t_3;
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2075
- * # as the sequence is stored in half-bytes, the total length (sequence
- * # plus quality scores) is (l+1)/2 + l
- * nbytes_new = (l+1)/2 + l # <<<<<<<<<<<<<<
- * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
- * # acquire pointer to location in memory
+ /* "csamtools.pyx":1959
+ * raise StopIteration
+ *
+ * if self.truncate: # <<<<<<<<<<<<<<
+ * if self.start < self.pos: continue
+ * if self.pos >= self.end: raise StopIteration
*/
- __pyx_v_nbytes_new = (__Pyx_div_long((__pyx_v_l + 1), 2) + __pyx_v_l);
+ if (__pyx_v_self->truncate) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2076
- * # plus quality scores) is (l+1)/2 + l
- * nbytes_new = (l+1)/2 + l
- * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq # <<<<<<<<<<<<<<
- * # acquire pointer to location in memory
- * p = bam1_seq( src )
+ /* "csamtools.pyx":1960
+ *
+ * if self.truncate:
+ * if self.start < self.pos: continue # <<<<<<<<<<<<<<
+ * if self.pos >= self.end: raise StopIteration
+ *
*/
- __pyx_v_nbytes_old = (__Pyx_div_long((__pyx_v_src->core.l_qseq + 1), 2) + __pyx_v_src->core.l_qseq);
+ __pyx_t_1 = (__pyx_v_self->start < __pyx_v_self->__pyx_base.pos);
+ if (__pyx_t_1) {
+ goto __pyx_L3_continue;
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2078
- * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
- * # acquire pointer to location in memory
- * p = bam1_seq( src ) # <<<<<<<<<<<<<<
- * src.core.l_qseq = l
+ /* "csamtools.pyx":1961
+ * if self.truncate:
+ * if self.start < self.pos: continue
+ * if self.pos >= self.end: raise StopIteration # <<<<<<<<<<<<<<
*
+ * return makePileupProxy( &self.plp,
*/
- __pyx_v_p = bam1_seq(__pyx_v_src);
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.pos >= __pyx_v_self->end);
+ if (__pyx_t_1) {
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2079
- * # acquire pointer to location in memory
- * p = bam1_seq( src )
- * src.core.l_qseq = l # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1963
+ * if self.pos >= self.end: raise StopIteration
*
- * pysam_bam_update( src,
+ * return makePileupProxy( &self.plp, # <<<<<<<<<<<<<<
+ * self.tid,
+ * self.pos,
*/
- __pyx_v_src->core.l_qseq = __pyx_v_l;
+ __Pyx_XDECREF(__pyx_r);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2084
- * nbytes_old,
- * nbytes_new,
- * p) # <<<<<<<<<<<<<<
- * # re-acquire pointer to location in memory
- * # as it might have moved
+ /* "csamtools.pyx":1966
+ * self.tid,
+ * self.pos,
+ * self.n_plp ) # <<<<<<<<<<<<<<
+ *
+ * cdef class IteratorColumnAllRefs(IteratorColumn):
*/
- pysam_bam_update(__pyx_v_src, __pyx_v_nbytes_old, __pyx_v_nbytes_new, __pyx_v_p);
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ __pyx_L3_continue:;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2087
- * # re-acquire pointer to location in memory
- * # as it might have moved
- * p = bam1_seq( src ) # <<<<<<<<<<<<<<
- * for k from 0 <= k < nbytes_new: p[k] = 0
- * # convert to C string
- */
- __pyx_v_p = bam1_seq(__pyx_v_src);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2088
- * # as it might have moved
- * p = bam1_seq( src )
- * for k from 0 <= k < nbytes_new: p[k] = 0 # <<<<<<<<<<<<<<
- * # convert to C string
- * s = seq
- */
- __pyx_t_6 = __pyx_v_nbytes_new;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
- (__pyx_v_p[__pyx_v_k]) = 0;
+/* Python wrapper */
+static int __pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ {
+ PyObject* values[1] = {0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ }
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
}
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2090
- * for k from 0 <= k < nbytes_new: p[k] = 0
- * # convert to C string
- * s = seq # <<<<<<<<<<<<<<
- * for k from 0 <= k < l:
- * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
- */
- __pyx_t_7 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_s = __pyx_t_7;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2091
- * # convert to C string
- * s = seq
- * for k from 0 <= k < l: # <<<<<<<<<<<<<<
- * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
+/* "csamtools.pyx":1972
+ * """
*
+ * def __cinit__(self, # <<<<<<<<<<<<<<
+ * Samfile samfile,
+ * **kwargs ):
*/
- __pyx_t_6 = __pyx_v_l;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2092
- * s = seq
- * for k from 0 <= k < l:
- * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) # <<<<<<<<<<<<<<
- *
- * # erase qualities
- */
- (__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) |= (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2))));
- }
+static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1972);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2095
+ /* "csamtools.pyx":1977
*
- * # erase qualities
- * p = bam1_qual( src ) # <<<<<<<<<<<<<<
- * p[0] = 0xff
+ * # no iteration over empty files
+ * if not samfile.nreferences: raise StopIteration # <<<<<<<<<<<<<<
*
+ * # initialize iterator
*/
- __pyx_v_p = bam1_qual(__pyx_v_src);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = (!__pyx_t_2);
+ if (__pyx_t_3) {
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2096
- * # erase qualities
- * p = bam1_qual( src )
- * p[0] = 0xff # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":1980
*
+ * # initialize iterator
+ * self.setupIteratorData( self.tid, 0, max_pos, 1 ) # <<<<<<<<<<<<<<
*
+ * def __next__(self):
*/
- (__pyx_v_p[0]) = 0xff;
+ __pyx_t_4.__pyx_n = 1;
+ __pyx_t_4.reopen = 1;
+ __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.seq.__set__");
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2101
- * property qual:
- * """read sequence base qualities, including :term:`soft clipped` bases (None if not present)"""
- * def __get__(self): # <<<<<<<<<<<<<<
- *
- * cdef bam1_t * src
- */
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__;
+static PyObject *__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
+/* "csamtools.pyx":1982
+ * self.setupIteratorData( self.tid, 0, max_pos, 1 )
+ *
+ * def __next__(self): # <<<<<<<<<<<<<<
+ * """python version of next().
+ * """
+ */
+
+static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2101);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1982);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2106
- * cdef char * q
+ /* "csamtools.pyx":1986
+ * """
*
- * src = self._delegate # <<<<<<<<<<<<<<
+ * while 1: # <<<<<<<<<<<<<<
+ * self.cnext()
*
- * if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ while (1) {
+ if (!1) break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2108
- * src = self._delegate
+ /* "csamtools.pyx":1987
*
- * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ * while 1:
+ * self.cnext() # <<<<<<<<<<<<<<
*
- * return get_qual_range(src, 0, src.core.l_qseq)
+ * if self.n_plp < 0:
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2110
- * if src.core.l_qseq == 0: return None
+ /* "csamtools.pyx":1989
+ * self.cnext()
*
- * return get_qual_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
+ * if self.n_plp < 0: # <<<<<<<<<<<<<<
+ * raise ValueError("error during iteration" )
*
- * def __set__(self,qual):
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":1990
+ *
+ * if self.n_plp < 0:
+ * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
+ *
+ * # return result, if within same reference
+ */
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_131), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
+
+ /* "csamtools.pyx":1993
+ *
+ * # return result, if within same reference
+ * if self.plp != NULL: # <<<<<<<<<<<<<<
+ * return makePileupProxy( &self.plp,
+ * self.tid,
+ */
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":1994
+ * # return result, if within same reference
+ * if self.plp != NULL:
+ * return makePileupProxy( &self.plp, # <<<<<<<<<<<<<<
+ * self.tid,
+ * self.pos,
+ */
+ __Pyx_XDECREF(__pyx_r);
+
+ /* "csamtools.pyx":1997
+ * self.tid,
+ * self.pos,
+ * self.n_plp ) # <<<<<<<<<<<<<<
+ *
+ * # otherwise, proceed to next reference or stop
+ */
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+
+ /* "csamtools.pyx":2000
+ *
+ * # otherwise, proceed to next reference or stop
+ * self.tid += 1 # <<<<<<<<<<<<<<
+ * if self.tid < self.samfile.nreferences:
+ * self.setupIteratorData( self.tid, 0, max_pos, 0 )
+ */
+ __pyx_v_self->__pyx_base.tid = (__pyx_v_self->__pyx_base.tid + 1);
+
+ /* "csamtools.pyx":2001
+ * # otherwise, proceed to next reference or stop
+ * self.tid += 1
+ * if self.tid < self.samfile.nreferences: # <<<<<<<<<<<<<<
+ * self.setupIteratorData( self.tid, 0, max_pos, 0 )
+ * else:
+ */
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_self->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":2002
+ * self.tid += 1
+ * if self.tid < self.samfile.nreferences:
+ * self.setupIteratorData( self.tid, 0, max_pos, 0 ) # <<<<<<<<<<<<<<
+ * else:
+ * raise StopIteration
+ */
+ __pyx_t_5.__pyx_n = 1;
+ __pyx_t_5.reopen = 0;
+ __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ goto __pyx_L7;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2004
+ * self.setupIteratorData( self.tid, 0, max_pos, 0 )
+ * else:
+ * raise StopIteration # <<<<<<<<<<<<<<
+ *
+ * ##-------------------------------------------------------------------
+ */
+ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L7:;
+ }
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qual.__get__");
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2112
- * return get_qual_range(src, 0, src.core.l_qseq)
- *
- * def __set__(self,qual): # <<<<<<<<<<<<<<
- * # note that space is already allocated via the sequences
- * cdef bam1_t * src
+/* "csamtools.pyx":2009
+ * ##-------------------------------------------------------------------
+ * ##-------------------------------------------------------------------
+ * cdef inline int32_t query_start(bam1_t *src) except -1: # <<<<<<<<<<<<<<
+ * cdef uint32_t * cigar_p, op
+ * cdef uint32_t k
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4qual___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4qual___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
- bam1_t *__pyx_v_src;
- uint8_t *__pyx_v_p;
- char *__pyx_v_q;
- int __pyx_v_k;
- int __pyx_v_l;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) {
+ uint32_t *__pyx_v_cigar_p;
+ uint32_t __pyx_v_op;
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_start_offset;
+ int32_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ uint32_t __pyx_t_1;
int __pyx_t_2;
- Py_ssize_t __pyx_t_3;
+ int __pyx_t_3;
int __pyx_t_4;
- int __pyx_t_5;
- char *__pyx_t_6;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
+ PyObject *__pyx_t_5 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2112);
+ __Pyx_RefNannySetupContext("query_start", 0);
+ __Pyx_TraceCall("query_start", __pyx_f[0], 2009);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2119
- * cdef int k
+ /* "csamtools.pyx":2012
+ * cdef uint32_t * cigar_p, op
+ * cdef uint32_t k
+ * cdef uint32_t start_offset = 0 # <<<<<<<<<<<<<<
*
- * src = self._delegate # <<<<<<<<<<<<<<
- * p = bam1_qual( src )
- * if qual == None or len(qual) == 0:
+ * if src.core.n_cigar:
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_v_start_offset = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2120
+ /* "csamtools.pyx":2014
+ * cdef uint32_t start_offset = 0
*
- * src = self._delegate
- * p = bam1_qual( src ) # <<<<<<<<<<<<<<
- * if qual == None or len(qual) == 0:
- * # if absent - set to 0xff
- */
- __pyx_v_p = bam1_qual(__pyx_v_src);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2121
- * src = self._delegate
- * p = bam1_qual( src )
- * if qual == None or len(qual) == 0: # <<<<<<<<<<<<<<
- * # if absent - set to 0xff
- * p[0] = 0xff
+ * if src.core.n_cigar: # <<<<<<<<<<<<<<
+ * cigar_p = bam1_cigar(src);
+ * for k from 0 <= k < src.core.n_cigar:
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = (__pyx_t_3 == 0);
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_2;
- }
- if (__pyx_t_5) {
+ if (__pyx_v_src->core.n_cigar) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2123
- * if qual == None or len(qual) == 0:
- * # if absent - set to 0xff
- * p[0] = 0xff # <<<<<<<<<<<<<<
- * return
- * cdef int l
+ /* "csamtools.pyx":2015
+ *
+ * if src.core.n_cigar:
+ * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
*/
- (__pyx_v_p[0]) = 0xff;
+ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2124
- * # if absent - set to 0xff
- * p[0] = 0xff
- * return # <<<<<<<<<<<<<<
- * cdef int l
- * # convert to C string
+ /* "csamtools.pyx":2016
+ * if src.core.n_cigar:
+ * cigar_p = bam1_cigar(src);
+ * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if op==BAM_CHARD_CLIP:
*/
- __pyx_r = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_1 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2127
- * cdef int l
- * # convert to C string
- * q = qual # <<<<<<<<<<<<<<
- * l = len(qual)
- * if src.core.l_qseq != l:
+ /* "csamtools.pyx":2017
+ * cigar_p = bam1_cigar(src);
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
+ * if op==BAM_CHARD_CLIP:
+ * if start_offset!=0 and start_offset!=src.core.l_qseq:
*/
- __pyx_t_6 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_q = __pyx_t_6;
+ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2128
- * # convert to C string
- * q = qual
- * l = len(qual) # <<<<<<<<<<<<<<
- * if src.core.l_qseq != l:
- * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
+ /* "csamtools.pyx":2022
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1
+ * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
+ * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
+ * else:
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_l = __pyx_t_3;
+ switch (__pyx_v_op) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2129
- * q = qual
- * l = len(qual)
- * if src.core.l_qseq != l: # <<<<<<<<<<<<<<
- * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
- * assert src.core.l_qseq == l
+ /* "csamtools.pyx":2018
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
+ * if start_offset!=0 and start_offset!=src.core.l_qseq:
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
*/
- __pyx_t_5 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
- if (__pyx_t_5) {
+ case 5:
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2130
- * l = len(qual)
- * if src.core.l_qseq != l:
- * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) # <<<<<<<<<<<<<<
- * assert src.core.l_qseq == l
- * for k from 0 <= k < l:
+ /* "csamtools.pyx":2019
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if op==BAM_CHARD_CLIP:
+ * if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_1 = 0;
- __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_61), __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_2 = (__pyx_v_start_offset != 0);
+ if (__pyx_t_2) {
+ __pyx_t_3 = (__pyx_v_start_offset != __pyx_v_src->core.l_qseq);
+ __pyx_t_4 = __pyx_t_3;
+ } else {
+ __pyx_t_4 = __pyx_t_2;
+ }
+ if (__pyx_t_4) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2131
- * if src.core.l_qseq != l:
- * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
- * assert src.core.l_qseq == l # <<<<<<<<<<<<<<
- * for k from 0 <= k < l:
- * p[k] = <uint8_t>q[k] - 33
+ /* "csamtools.pyx":2020
+ * if op==BAM_CHARD_CLIP:
+ * if start_offset!=0 and start_offset!=src.core.l_qseq:
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
+ * return -1
+ * elif op==BAM_CSOFT_CLIP:
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_src->core.l_qseq == __pyx_v_l))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __pyx_t_5 = __pyx_builtin_ValueError;
+ __Pyx_INCREF(__pyx_t_5);
+ PyErr_SetString(__pyx_t_5, __pyx_k_132);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2132
- * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
- * assert src.core.l_qseq == l
- * for k from 0 <= k < l: # <<<<<<<<<<<<<<
- * p[k] = <uint8_t>q[k] - 33
- *
+ /* "csamtools.pyx":2021
+ * if start_offset!=0 and start_offset!=src.core.l_qseq:
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1 # <<<<<<<<<<<<<<
+ * elif op==BAM_CSOFT_CLIP:
+ * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_9 = __pyx_v_l;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_9; __pyx_v_k++) {
+ __pyx_r = -1;
+ goto __pyx_L0;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+ break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2133
- * assert src.core.l_qseq == l
- * for k from 0 <= k < l:
- * p[k] = <uint8_t>q[k] - 33 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2022
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1
+ * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
+ * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
+ * else:
+ */
+ case 4:
+
+ /* "csamtools.pyx":2023
+ * return -1
+ * elif op==BAM_CSOFT_CLIP:
+ * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
+ * else:
+ * break
+ */
+ __pyx_v_start_offset = (__pyx_v_start_offset + ((__pyx_v_cigar_p[__pyx_v_k]) >> 4));
+ break;
+ default:
+
+ /* "csamtools.pyx":2025
+ * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
+ * else:
+ * break # <<<<<<<<<<<<<<
*
- * property query:
+ * return start_offset
*/
- (__pyx_v_p[__pyx_v_k]) = (((uint8_t)(__pyx_v_q[__pyx_v_k])) - 33);
+ goto __pyx_L5_break;
+ break;
+ }
+ }
+ __pyx_L5_break:;
+ goto __pyx_L3;
}
+ __pyx_L3:;
- __pyx_r = 0;
+ /* "csamtools.pyx":2027
+ * break
+ *
+ * return start_offset # <<<<<<<<<<<<<<
+ *
+ * ##-------------------------------------------------------------------
+ */
+ __pyx_r = __pyx_v_start_offset;
goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.AlignedRead.qual.__set__");
- __pyx_r = -1;
+
+ __pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2145
- * were not considered for alignment may have been retained."""
- *
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * cdef uint32_t start, end
+/* "csamtools.pyx":2032
+ * ##-------------------------------------------------------------------
+ * ##-------------------------------------------------------------------
+ * cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
+ * cdef uint32_t * cigar_p, op
+ * cdef uint32_t k
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
- uint32_t __pyx_v_start;
- uint32_t __pyx_v_end;
- PyObject *__pyx_r = NULL;
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
+ uint32_t *__pyx_v_cigar_p;
+ uint32_t __pyx_v_op;
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_end_offset;
+ int32_t __pyx_r;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
- int32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2145);
+ __Pyx_RefNannySetupContext("query_end", 0);
+ __Pyx_TraceCall("query_end", __pyx_f[0], 2032);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2150
- * cdef char * s
- *
- * src = self._delegate # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2035
+ * cdef uint32_t * cigar_p, op
+ * cdef uint32_t k
+ * cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
- * if src.core.l_qseq == 0: return None
+ * if src.core.n_cigar>1:
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2152
- * src = self._delegate
- *
- * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2037
+ * cdef uint32_t end_offset = src.core.l_qseq
*
- * start = query_start(src)
+ * if src.core.n_cigar>1: # <<<<<<<<<<<<<<
+ * cigar_p = bam1_cigar(src);
+ * for k from src.core.n_cigar > k >= 1:
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar > 1);
if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2154
- * if src.core.l_qseq == 0: return None
- *
- * start = query_start(src) # <<<<<<<<<<<<<<
- * end = query_end(src)
+ /* "csamtools.pyx":2038
*
+ * if src.core.n_cigar>1:
+ * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
+ * for k from src.core.n_cigar > k >= 1:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_start = __pyx_t_2;
+ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2155
- *
- * start = query_start(src)
- * end = query_end(src) # <<<<<<<<<<<<<<
- *
- * return get_seq_range(src, start, end)
+ /* "csamtools.pyx":2039
+ * if src.core.n_cigar>1:
+ * cigar_p = bam1_cigar(src);
+ * for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<<
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if op==BAM_CHARD_CLIP:
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_end = __pyx_t_2;
+ for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2157
- * end = query_end(src)
- *
- * return get_seq_range(src, start, end) # <<<<<<<<<<<<<<
- *
- * property qqual:
+ /* "csamtools.pyx":2040
+ * cigar_p = bam1_cigar(src);
+ * for k from src.core.n_cigar > k >= 1:
+ * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
+ * if op==BAM_CHARD_CLIP:
+ * if end_offset!=0 and end_offset!=src.core.l_qseq:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
+ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.AlignedRead.query.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2045
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1
+ * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
+ * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
+ * else:
+ */
+ switch (__pyx_v_op) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2161
- * property qqual:
- * """aligned query sequence quality values (None if not present)"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * cdef uint32_t start, end
+ /* "csamtools.pyx":2041
+ * for k from src.core.n_cigar > k >= 1:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
+ * if end_offset!=0 and end_offset!=src.core.l_qseq:
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
*/
+ case 5:
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
- uint32_t __pyx_v_start;
- uint32_t __pyx_v_end;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- int32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2161);
+ /* "csamtools.pyx":2042
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if op==BAM_CHARD_CLIP:
+ * if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1
+ */
+ __pyx_t_1 = (__pyx_v_end_offset != 0);
+ if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
+ __pyx_t_3 = __pyx_t_2;
+ } else {
+ __pyx_t_3 = __pyx_t_1;
+ }
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2166
- * cdef char * q
- *
- * src = self._delegate # <<<<<<<<<<<<<<
- *
- * if src.core.l_qseq == 0: return None
+ /* "csamtools.pyx":2043
+ * if op==BAM_CHARD_CLIP:
+ * if end_offset!=0 and end_offset!=src.core.l_qseq:
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
+ * return -1
+ * elif op==BAM_CSOFT_CLIP:
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_4 = __pyx_builtin_ValueError;
+ __Pyx_INCREF(__pyx_t_4);
+ PyErr_SetString(__pyx_t_4, __pyx_k_132);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2168
- * src = self._delegate
- *
- * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2044
+ * if end_offset!=0 and end_offset!=src.core.l_qseq:
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1 # <<<<<<<<<<<<<<
+ * elif op==BAM_CSOFT_CLIP:
+ * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
+ */
+ __pyx_r = -1;
+ goto __pyx_L0;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+ break;
+
+ /* "csamtools.pyx":2045
+ * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
+ * return -1
+ * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
+ * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
+ * else:
+ */
+ case 4:
+
+ /* "csamtools.pyx":2046
+ * return -1
+ * elif op==BAM_CSOFT_CLIP:
+ * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
+ * else:
+ * break
+ */
+ __pyx_v_end_offset = (__pyx_v_end_offset - ((__pyx_v_cigar_p[__pyx_v_k]) >> 4));
+ break;
+ default:
+
+ /* "csamtools.pyx":2048
+ * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
+ * else:
+ * break # <<<<<<<<<<<<<<
*
- * start = query_start(src)
+ * if end_offset==0:
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L5_break;
+ break;
+ }
+ }
+ __pyx_L5_break:;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2170
- * if src.core.l_qseq == 0: return None
+ /* "csamtools.pyx":2050
+ * break
*
- * start = query_start(src) # <<<<<<<<<<<<<<
- * end = query_end(src)
+ * if end_offset==0: # <<<<<<<<<<<<<<
+ * end_offset = src.core.l_qseq
*
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_start = __pyx_t_2;
+ __pyx_t_3 = (__pyx_v_end_offset == 0);
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2171
+ /* "csamtools.pyx":2051
*
- * start = query_start(src)
- * end = query_end(src) # <<<<<<<<<<<<<<
+ * if end_offset==0:
+ * end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
- * return get_qual_range(src, start, end)
+ * return end_offset
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_end = __pyx_t_2;
+ __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2173
- * end = query_end(src)
+ /* "csamtools.pyx":2053
+ * end_offset = src.core.l_qseq
+ *
+ * return end_offset # <<<<<<<<<<<<<<
*
- * return get_qual_range(src, start, end) # <<<<<<<<<<<<<<
*
- * property qstart:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_r = __pyx_v_end_offset;
goto __pyx_L0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.AlignedRead.qqual.__get__");
- __pyx_r = NULL;
+ __pyx_r = 0;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2177
- * property qstart:
- * """start index of the aligned query portion of the sequence (0-based, inclusive)"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * return query_start(self._delegate)
+/* "csamtools.pyx":2056
*
+ *
+ * cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
+ * cdef uint8_t * p
+ * cdef uint32_t k
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self) {
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+ uint8_t *__pyx_v_p;
+ uint32_t __pyx_v_k;
+ char *__pyx_v_s;
+ PyObject *__pyx_v_seq = NULL;
PyObject *__pyx_r = NULL;
- int32_t __pyx_t_1;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
+ char *__pyx_t_3;
+ uint32_t __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2177);
+ __Pyx_RefNannySetupContext("get_seq_range", 0);
+ __Pyx_TraceCall("get_seq_range", __pyx_f[0], 2056);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2178
- * """start index of the aligned query portion of the sequence (0-based, inclusive)"""
- * def __get__(self):
- * return query_start(self._delegate) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2061
+ * cdef char * s
+ *
+ * if not src.core.l_qseq: # <<<<<<<<<<<<<<
+ * return None
*
- * property qend:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_start(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (!__pyx_v_src->core.l_qseq);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":2062
+ *
+ * if not src.core.l_qseq:
+ * return None # <<<<<<<<<<<<<<
+ *
+ * seq = PyBytes_FromStringAndSize(NULL, end - start)
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2064
+ * return None
+ *
+ * seq = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
+ * s = <char*>seq
+ * p = bam1_seq(src)
+ */
+ __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
+ __pyx_v_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- goto __pyx_L0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qstart.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2065
+ *
+ * seq = PyBytes_FromStringAndSize(NULL, end - start)
+ * s = <char*>seq # <<<<<<<<<<<<<<
+ * p = bam1_seq(src)
+ *
+ */
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2065; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = ((char *)__pyx_t_3);
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2182
- * property qend:
- * """end index of the aligned query portion of the sequence (0-based, exclusive)"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * return query_end(self._delegate)
+ /* "csamtools.pyx":2066
+ * seq = PyBytes_FromStringAndSize(NULL, end - start)
+ * s = <char*>seq
+ * p = bam1_seq(src) # <<<<<<<<<<<<<<
*
+ * for k from start <= k < end:
*/
+ __pyx_v_p = bam1_seq(__pyx_v_src);
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- int32_t __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2182);
+ /* "csamtools.pyx":2068
+ * p = bam1_seq(src)
+ *
+ * for k from start <= k < end: # <<<<<<<<<<<<<<
+ * # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
+ * # note: do not use string literal as it will be a python string
+ */
+ __pyx_t_4 = __pyx_v_end;
+ for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2183
- * """end index of the aligned query portion of the sequence (0-based, exclusive)"""
- * def __get__(self):
- * return query_end(self._delegate) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2071
+ * # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
+ * # note: do not use string literal as it will be a python string
+ * s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] # <<<<<<<<<<<<<<
+ *
+ * return seq
+ */
+ (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
+ }
+
+ /* "csamtools.pyx":2073
+ * s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf]
+ *
+ * return seq # <<<<<<<<<<<<<<
+ *
*
- * property qlen:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_end(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_v_seq));
+ __pyx_r = ((PyObject *)__pyx_v_seq);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qend.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.get_seq_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_seq);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2187
- * property qlen:
- * """Length of the aligned query sequence"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * src = self._delegate
+/* "csamtools.pyx":2076
+ *
+ *
+ * cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
+ * cdef uint8_t * p
+ * cdef uint32_t k
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+ uint8_t *__pyx_v_p;
+ uint32_t __pyx_v_k;
+ char *__pyx_v_q;
+ PyObject *__pyx_v_qual = NULL;
PyObject *__pyx_r = NULL;
- int32_t __pyx_t_1;
- int32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ char *__pyx_t_3;
+ uint32_t __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2187);
+ __Pyx_RefNannySetupContext("get_qual_range", 0);
+ __Pyx_TraceCall("get_qual_range", __pyx_f[0], 2076);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2189
- * def __get__(self):
- * cdef bam1_t * src
- * src = self._delegate # <<<<<<<<<<<<<<
- * return query_end(src)-query_start(src)
+ /* "csamtools.pyx":2081
+ * cdef char * q
*
+ * p = bam1_qual(src) # <<<<<<<<<<<<<<
+ * if p[0] == 0xff:
+ * return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_v_p = bam1_qual(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2190
- * cdef bam1_t * src
- * src = self._delegate
- * return query_end(src)-query_start(src) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2082
*
- * property tags:
+ * p = bam1_qual(src)
+ * if p[0] == 0xff: # <<<<<<<<<<<<<<
+ * return None
+ *
+ */
+ __pyx_t_1 = ((__pyx_v_p[0]) == 0xff);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":2083
+ * p = bam1_qual(src)
+ * if p[0] == 0xff:
+ * return None # <<<<<<<<<<<<<<
+ *
+ * qual = PyBytes_FromStringAndSize(NULL, end - start)
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2085
+ * return None
+ *
+ * qual = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
+ * q = <char*>qual
+ *
+ */
+ __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_qual = ((PyObject*)__pyx_t_2);
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":2086
+ *
+ * qual = PyBytes_FromStringAndSize(NULL, end - start)
+ * q = <char*>qual # <<<<<<<<<<<<<<
+ *
+ * for k from start <= k < end:
+ */
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_q = ((char *)__pyx_t_3);
+
+ /* "csamtools.pyx":2088
+ * q = <char*>qual
+ *
+ * for k from start <= k < end: # <<<<<<<<<<<<<<
+ * ## equivalent to t[i] + 33 (see bam.c)
+ * q[k-start] = p[k] + 33
+ */
+ __pyx_t_4 = __pyx_v_end;
+ for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
+
+ /* "csamtools.pyx":2090
+ * for k from start <= k < end:
+ * ## equivalent to t[i] + 33 (see bam.c)
+ * q[k-start] = p[k] + 33 # <<<<<<<<<<<<<<
+ *
+ * return qual
+ */
+ (__pyx_v_q[(__pyx_v_k - __pyx_v_start)]) = ((__pyx_v_p[__pyx_v_k]) + 33);
+ }
+
+ /* "csamtools.pyx":2092
+ * q[k-start] = p[k] + 33
+ *
+ * return qual # <<<<<<<<<<<<<<
+ *
+ * cdef class AlignedRead:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyInt_to_py_int32_t((__pyx_t_1 - __pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_v_qual));
+ __pyx_r = ((PyObject *)__pyx_v_qual);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.AlignedRead.qlen.__get__");
- __pyx_r = NULL;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.get_qual_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = 0;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_qual);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2204
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead___init__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2124
*
- * """
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef char * ctag
- * cdef bam1_t * src
+ * # Now only called when instances are created from Python
+ * def __init__(self): # <<<<<<<<<<<<<<
+ * # see bam_init1
+ * self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) )
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self) {
- bam1_t *__pyx_v_src;
- uint8_t *__pyx_v_s;
- char __pyx_v_auxtag[3];
- char __pyx_v_auxtype;
- PyObject *__pyx_v_result;
- PyObject *__pyx_v_value;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- char __pyx_t_3;
- int __pyx_t_4;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- Py_ssize_t __pyx_t_7;
- int __pyx_t_8;
+static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2204);
- __pyx_v_result = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_value = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 2124);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2211
- * cdef char auxtype
- *
- * src = self._delegate # <<<<<<<<<<<<<<
- * if src.l_aux == 0: return None
- *
+ /* "csamtools.pyx":2126
+ * def __init__(self):
+ * # see bam_init1
+ * self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
+ * # allocate some memory
+ * # If size is 0, calloc does not return a pointer that can be passed to free()
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_v_self->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2212
- *
- * src = self._delegate
- * if src.l_aux == 0: return None # <<<<<<<<<<<<<<
- *
- * s = bam1_aux( src )
+ /* "csamtools.pyx":2130
+ * # If size is 0, calloc does not return a pointer that can be passed to free()
+ * # so allocate 40 bytes for a new read
+ * self._delegate.m_data = 40 # <<<<<<<<<<<<<<
+ * self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
+ * self._delegate.data_len = 0
*/
- __pyx_t_1 = (__pyx_v_src->l_aux == 0);
- if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_v_self->_delegate->m_data = 40;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2214
- * if src.l_aux == 0: return None
+ /* "csamtools.pyx":2131
+ * # so allocate 40 bytes for a new read
+ * self._delegate.m_data = 40
+ * self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 ) # <<<<<<<<<<<<<<
+ * self._delegate.data_len = 0
*
- * s = bam1_aux( src ) # <<<<<<<<<<<<<<
- * result = []
- * auxtag[2] = 0
*/
- __pyx_v_s = bam1_aux(__pyx_v_src);
+ __pyx_v_self->_delegate->data = ((uint8_t *)calloc(__pyx_v_self->_delegate->m_data, 1));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2215
+ /* "csamtools.pyx":2132
+ * self._delegate.m_data = 40
+ * self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
+ * self._delegate.data_len = 0 # <<<<<<<<<<<<<<
*
- * s = bam1_aux( src )
- * result = [] # <<<<<<<<<<<<<<
- * auxtag[2] = 0
- * while s < (src.data + src.data_len):
+ * def __dealloc__(self):
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(((PyObject *)__pyx_v_result));
- __pyx_v_result = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_self->_delegate->data_len = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2216
- * s = bam1_aux( src )
- * result = []
- * auxtag[2] = 0 # <<<<<<<<<<<<<<
- * while s < (src.data + src.data_len):
- * # get tag
- */
- (__pyx_v_auxtag[2]) = 0;
+ __pyx_r = 0;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2217
- * result = []
- * auxtag[2] = 0
- * while s < (src.data + src.data_len): # <<<<<<<<<<<<<<
- * # get tag
- * auxtag[0] = s[0]
- */
- while (1) {
- __pyx_t_1 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
- if (!__pyx_t_1) break;
+/* Python wrapper */
+static void __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2219
- * while s < (src.data + src.data_len):
- * # get tag
- * auxtag[0] = s[0] # <<<<<<<<<<<<<<
- * auxtag[1] = s[1]
- * s += 2
+/* "csamtools.pyx":2134
+ * self._delegate.data_len = 0
+ *
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * bam_destroy1(self._delegate)
+ *
*/
- (__pyx_v_auxtag[0]) = (__pyx_v_s[0]);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2220
- * # get tag
- * auxtag[0] = s[0]
- * auxtag[1] = s[1] # <<<<<<<<<<<<<<
- * s += 2
- * auxtype = s[0]
- */
- (__pyx_v_auxtag[1]) = (__pyx_v_s[1]);
+static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 2134);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2221
- * auxtag[0] = s[0]
- * auxtag[1] = s[1]
- * s += 2 # <<<<<<<<<<<<<<
- * auxtype = s[0]
+ /* "csamtools.pyx":2135
*
- */
- __pyx_v_s += 2;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2222
- * auxtag[1] = s[1]
- * s += 2
- * auxtype = s[0] # <<<<<<<<<<<<<<
+ * def __dealloc__(self):
+ * bam_destroy1(self._delegate) # <<<<<<<<<<<<<<
*
- * if auxtype in ('c', 'C'):
+ * def __str__(self):
*/
- __pyx_v_auxtype = (__pyx_v_s[0]);
+ bam_destroy1(__pyx_v_self->_delegate);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2224
- * auxtype = s[0]
- *
- * if auxtype in ('c', 'C'): # <<<<<<<<<<<<<<
- * value = <int>bam_aux2i(s)
- * s += 1
- */
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = (__pyx_t_3 == 'c');
- if (!__pyx_t_1) {
- __pyx_t_4 = (__pyx_t_3 == 'C');
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_1;
- }
- __pyx_t_1 = __pyx_t_5;
- if (__pyx_t_1) {
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2225
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_4__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__;
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4__str__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2137
+ * bam_destroy1(self._delegate)
+ *
+ * def __str__(self): # <<<<<<<<<<<<<<
+ * """return string representation of alignment.
*
- * if auxtype in ('c', 'C'):
- * value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
- * s += 1
- * elif auxtype in ('s', 'S'):
*/
- __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2226
- * if auxtype in ('c', 'C'):
- * value = <int>bam_aux2i(s)
- * s += 1 # <<<<<<<<<<<<<<
- * elif auxtype in ('s', 'S'):
- * value = <int>bam_aux2i(s)
- */
- __pyx_v_s += 1;
- goto __pyx_L8;
- }
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_v_seq = NULL;
+ PyObject *__pyx_v_qual = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ PyObject *__pyx_t_12 = NULL;
+ PyObject *__pyx_t_13 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 2137);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2227
- * value = <int>bam_aux2i(s)
- * s += 1
- * elif auxtype in ('s', 'S'): # <<<<<<<<<<<<<<
- * value = <int>bam_aux2i(s)
- * s += 2
+ /* "csamtools.pyx":2149
+ * # sam-parsing is done in sam.c/bam_format1_core which
+ * # requires a valid header.
+ * if sys.version_info[0] < 3: # <<<<<<<<<<<<<<
+ * seq = self.seq
+ * qual = self.qual
*/
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = (__pyx_t_3 == 's');
- if (!__pyx_t_1) {
- __pyx_t_5 = (__pyx_t_3 == 'S');
- __pyx_t_4 = __pyx_t_5;
- } else {
- __pyx_t_4 = __pyx_t_1;
- }
- __pyx_t_1 = __pyx_t_4;
- if (__pyx_t_1) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2228
- * s += 1
- * elif auxtype in ('s', 'S'):
- * value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
- * s += 2
- * elif auxtype in ('i', 'I'):
- */
- __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2229
- * elif auxtype in ('s', 'S'):
- * value = <int>bam_aux2i(s)
- * s += 2 # <<<<<<<<<<<<<<
- * elif auxtype in ('i', 'I'):
- * value = <float>bam_aux2i(s)
- */
- __pyx_v_s += 2;
- goto __pyx_L8;
- }
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2230
- * value = <int>bam_aux2i(s)
- * s += 2
- * elif auxtype in ('i', 'I'): # <<<<<<<<<<<<<<
- * value = <float>bam_aux2i(s)
- * s += 4
- */
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = (__pyx_t_3 == 'i');
- if (!__pyx_t_1) {
- __pyx_t_4 = (__pyx_t_3 == 'I');
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_1;
- }
- __pyx_t_1 = __pyx_t_5;
- if (__pyx_t_1) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2231
- * s += 2
- * elif auxtype in ('i', 'I'):
- * value = <float>bam_aux2i(s) # <<<<<<<<<<<<<<
- * s += 4
- * elif auxtype == 'f':
- */
- __pyx_t_2 = PyFloat_FromDouble(((float)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2232
- * elif auxtype in ('i', 'I'):
- * value = <float>bam_aux2i(s)
- * s += 4 # <<<<<<<<<<<<<<
- * elif auxtype == 'f':
- * value = <float>bam_aux2f(s)
- */
- __pyx_v_s += 4;
- goto __pyx_L8;
- }
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2233
- * value = <float>bam_aux2i(s)
- * s += 4
- * elif auxtype == 'f': # <<<<<<<<<<<<<<
- * value = <float>bam_aux2f(s)
- * s += 4
- */
- __pyx_t_1 = (__pyx_v_auxtype == 'f');
- if (__pyx_t_1) {
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__version_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_3, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2234
- * s += 4
- * elif auxtype == 'f':
- * value = <float>bam_aux2f(s) # <<<<<<<<<<<<<<
- * s += 4
- * elif auxtype == 'd':
+ /* "csamtools.pyx":2150
+ * # requires a valid header.
+ * if sys.version_info[0] < 3:
+ * seq = self.seq # <<<<<<<<<<<<<<
+ * qual = self.qual
+ * else:
*/
- __pyx_t_2 = PyFloat_FromDouble(bam_aux2f(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_seq = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2235
- * elif auxtype == 'f':
- * value = <float>bam_aux2f(s)
- * s += 4 # <<<<<<<<<<<<<<
- * elif auxtype == 'd':
- * value = <double>bam_aux2d(s)
+ /* "csamtools.pyx":2151
+ * if sys.version_info[0] < 3:
+ * seq = self.seq
+ * qual = self.qual # <<<<<<<<<<<<<<
+ * else:
+ * seq = self.seq.decode('ascii')
*/
- __pyx_v_s += 4;
- goto __pyx_L8;
- }
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_qual = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2236
- * value = <float>bam_aux2f(s)
- * s += 4
- * elif auxtype == 'd': # <<<<<<<<<<<<<<
- * value = <double>bam_aux2d(s)
- * s += 8
+ /* "csamtools.pyx":2153
+ * qual = self.qual
+ * else:
+ * seq = self.seq.decode('ascii') # <<<<<<<<<<<<<<
+ * qual = self.qual.decode('ascii')
+ * return "\t".join(map(str, (self.qname,
*/
- __pyx_t_1 = (__pyx_v_auxtype == 'd');
- if (__pyx_t_1) {
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_133), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_seq = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2237
- * s += 4
- * elif auxtype == 'd':
- * value = <double>bam_aux2d(s) # <<<<<<<<<<<<<<
- * s += 8
- * elif auxtype == 'A':
+ /* "csamtools.pyx":2154
+ * else:
+ * seq = self.seq.decode('ascii')
+ * qual = self.qual.decode('ascii') # <<<<<<<<<<<<<<
+ * return "\t".join(map(str, (self.qname,
+ * self.flag,
*/
- __pyx_t_2 = PyFloat_FromDouble(bam_aux2d(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_134), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_qual = __pyx_t_2;
+ __pyx_t_2 = 0;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2238
- * elif auxtype == 'd':
- * value = <double>bam_aux2d(s)
- * s += 8 # <<<<<<<<<<<<<<
- * elif auxtype == 'A':
- * value = "%c" % <char>bam_aux2A(s)
+ /* "csamtools.pyx":2155
+ * seq = self.seq.decode('ascii')
+ * qual = self.qual.decode('ascii')
+ * return "\t".join(map(str, (self.qname, # <<<<<<<<<<<<<<
+ * self.flag,
+ * self.rname,
*/
- __pyx_v_s += 8;
- goto __pyx_L8;
- }
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2239
- * value = <double>bam_aux2d(s)
- * s += 8
- * elif auxtype == 'A': # <<<<<<<<<<<<<<
- * value = "%c" % <char>bam_aux2A(s)
- * s += 1
+ /* "csamtools.pyx":2156
+ * qual = self.qual.decode('ascii')
+ * return "\t".join(map(str, (self.qname,
+ * self.flag, # <<<<<<<<<<<<<<
+ * self.rname,
+ * self.pos,
*/
- __pyx_t_1 = (__pyx_v_auxtype == 'A');
- if (__pyx_t_1) {
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2240
- * s += 8
- * elif auxtype == 'A':
- * value = "%c" % <char>bam_aux2A(s) # <<<<<<<<<<<<<<
- * s += 1
- * elif auxtype in ('Z', 'H'):
+ /* "csamtools.pyx":2157
+ * return "\t".join(map(str, (self.qname,
+ * self.flag,
+ * self.rname, # <<<<<<<<<<<<<<
+ * self.pos,
+ * self.mapq,
*/
- __pyx_t_2 = PyInt_FromLong(bam_aux2A(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_62), __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = ((PyObject *)__pyx_t_6);
- __pyx_t_6 = 0;
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2241
- * elif auxtype == 'A':
- * value = "%c" % <char>bam_aux2A(s)
- * s += 1 # <<<<<<<<<<<<<<
- * elif auxtype in ('Z', 'H'):
- * value = <char*>bam_aux2Z(s)
+ /* "csamtools.pyx":2158
+ * self.flag,
+ * self.rname,
+ * self.pos, # <<<<<<<<<<<<<<
+ * self.mapq,
+ * self.cigar,
*/
- __pyx_v_s += 1;
- goto __pyx_L8;
- }
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2242
- * value = "%c" % <char>bam_aux2A(s)
- * s += 1
- * elif auxtype in ('Z', 'H'): # <<<<<<<<<<<<<<
- * value = <char*>bam_aux2Z(s)
- * # +1 for NULL terminated string
+ /* "csamtools.pyx":2159
+ * self.rname,
+ * self.pos,
+ * self.mapq, # <<<<<<<<<<<<<<
+ * self.cigar,
+ * self.mrnm,
*/
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = (__pyx_t_3 == 'Z');
- if (!__pyx_t_1) {
- __pyx_t_5 = (__pyx_t_3 == 'H');
- __pyx_t_4 = __pyx_t_5;
- } else {
- __pyx_t_4 = __pyx_t_1;
- }
- __pyx_t_1 = __pyx_t_4;
- if (__pyx_t_1) {
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2243
- * s += 1
- * elif auxtype in ('Z', 'H'):
- * value = <char*>bam_aux2Z(s) # <<<<<<<<<<<<<<
- * # +1 for NULL terminated string
- * s += len(value) + 1
+ /* "csamtools.pyx":2160
+ * self.pos,
+ * self.mapq,
+ * self.cigar, # <<<<<<<<<<<<<<
+ * self.mrnm,
+ * self.mpos,
*/
- __pyx_t_6 = PyBytes_FromString(bam_aux2Z(__pyx_v_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = ((PyObject *)__pyx_t_6);
- __pyx_t_6 = 0;
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2245
- * value = <char*>bam_aux2Z(s)
- * # +1 for NULL terminated string
- * s += len(value) + 1 # <<<<<<<<<<<<<<
- * #
- * s += 1
+ /* "csamtools.pyx":2161
+ * self.mapq,
+ * self.cigar,
+ * self.mrnm, # <<<<<<<<<<<<<<
+ * self.mpos,
+ * self.rlen,
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_s += (__pyx_t_7 + 1);
- goto __pyx_L8;
- }
- __pyx_L8:;
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2247
- * s += len(value) + 1
- * #
- * s += 1 # <<<<<<<<<<<<<<
- *
- * result.append( (auxtag, value) )
+ /* "csamtools.pyx":2162
+ * self.cigar,
+ * self.mrnm,
+ * self.mpos, # <<<<<<<<<<<<<<
+ * self.rlen,
+ * seq,
*/
- __pyx_v_s += 1;
+ __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2249
- * s += 1
- *
- * result.append( (auxtag, value) ) # <<<<<<<<<<<<<<
- *
- * return result
+ /* "csamtools.pyx":2163
+ * self.mrnm,
+ * self.mpos,
+ * self.rlen, # <<<<<<<<<<<<<<
+ * seq,
+ * qual,
*/
- if (unlikely(__pyx_v_result == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = PyBytes_FromString(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_value);
- __Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_6 = 0;
- __pyx_t_8 = PyList_Append(((PyObject *)__pyx_v_result), __pyx_t_2); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- }
+ __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2251
- * result.append( (auxtag, value) )
- *
- * return result # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2166
+ * seq,
+ * qual,
+ * self.tags ))) # <<<<<<<<<<<<<<
*
- * def __set__(self, tags):
+ * def compare(self, AlignedRead other):
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_result));
- __pyx_r = ((PyObject *)__pyx_v_result);
+ __pyx_t_12 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
+ __pyx_t_13 = PyTuple_New(12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_13, 2, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_13, 3, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_13, 4, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_13, 5, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_13, 6, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_13, 7, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_13, 8, __pyx_t_11);
+ __Pyx_GIVEREF(__pyx_t_11);
+ __Pyx_INCREF(__pyx_v_seq);
+ PyTuple_SET_ITEM(__pyx_t_13, 9, __pyx_v_seq);
+ __Pyx_GIVEREF(__pyx_v_seq);
+ __Pyx_INCREF(__pyx_v_qual);
+ PyTuple_SET_ITEM(__pyx_t_13, 10, __pyx_v_qual);
+ __Pyx_GIVEREF(__pyx_v_qual);
+ PyTuple_SET_ITEM(__pyx_t_13, 11, __pyx_t_12);
+ __Pyx_GIVEREF(__pyx_t_12);
+ __pyx_t_1 = 0;
+ __pyx_t_4 = 0;
+ __pyx_t_5 = 0;
+ __pyx_t_6 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_10 = 0;
+ __pyx_t_11 = 0;
+ __pyx_t_12 = 0;
+ __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_12, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_12, 1, ((PyObject *)__pyx_t_13));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_13));
+ __pyx_t_13 = 0;
+ __pyx_t_13 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
+ __pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
+ PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_13);
+ __Pyx_GIVEREF(__pyx_t_13);
+ __pyx_t_13 = 0;
+ __pyx_t_13 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
+ __pyx_r = __pyx_t_13;
+ __pyx_t_13 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("csamtools.AlignedRead.tags.__get__");
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_XDECREF(__pyx_t_12);
+ __Pyx_XDECREF(__pyx_t_13);
+ __Pyx_AddTraceback("csamtools.AlignedRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_result);
- __Pyx_DECREF(__pyx_v_value);
+ __Pyx_XDECREF(__pyx_v_seq);
+ __Pyx_XDECREF(__pyx_v_qual);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2253
- * return result
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_6compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("compare (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_6compare(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2168
+ * self.tags )))
+ *
+ * def compare(self, AlignedRead other): # <<<<<<<<<<<<<<
+ * '''return -1,0,1, if contents in this are binary <,=,> to *other*'''
*
- * def __set__(self, tags): # <<<<<<<<<<<<<<
- * cdef char * ctag
- * cdef bam1_t * src
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tags___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tags___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
- bam1_t *__pyx_v_src;
- uint8_t *__pyx_v_s;
- char *__pyx_v_temp;
- int __pyx_v_max_size;
- int __pyx_v_size;
- int __pyx_v_offset;
- PyObject *__pyx_v_buffer;
- PyObject *__pyx_v_pytag;
- PyObject *__pyx_v_value;
- PyObject *__pyx_v_t;
- PyObject *__pyx_v_fmt;
- PyObject *__pyx_v_pytype;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- Py_ssize_t __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- Py_ssize_t __pyx_t_8;
- int __pyx_t_9;
- PyObject *__pyx_t_10 = NULL;
- char *__pyx_t_11;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other) {
+ int __pyx_v_retval;
+ bam1_t *__pyx_v_t;
+ bam1_t *__pyx_v_o;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2253);
- __pyx_v_buffer = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_pytag = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_value = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_t = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_fmt = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_pytype = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2262
- * cdef int max_size, size, offset
+ __Pyx_RefNannySetupContext("compare", 0);
+ __Pyx_TraceCall("compare", __pyx_f[0], 2168);
+
+ /* "csamtools.pyx":2174
+ * cdef bam1_t *t, *o
+ *
+ * t = self._delegate # <<<<<<<<<<<<<<
+ * o = other._delegate
*
- * src = self._delegate # <<<<<<<<<<<<<<
- * max_size = 4000
- * offset = 0
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_v_t = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2263
+ /* "csamtools.pyx":2175
*
- * src = self._delegate
- * max_size = 4000 # <<<<<<<<<<<<<<
- * offset = 0
+ * t = self._delegate
+ * o = other._delegate # <<<<<<<<<<<<<<
*
+ * # uncomment for debugging purposes
*/
- __pyx_v_max_size = 4000;
+ __pyx_v_o = __pyx_v_other->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2264
- * src = self._delegate
- * max_size = 4000
- * offset = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2187
+ *
+ * # Fast-path test for object identity
+ * if t==o: # <<<<<<<<<<<<<<
+ * return 0
*
- * if tags != None:
*/
- __pyx_v_offset = 0;
+ __pyx_t_1 = (__pyx_v_t == __pyx_v_o);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2266
- * offset = 0
- *
- * if tags != None: # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2188
+ * # Fast-path test for object identity
+ * if t==o:
+ * return 0 # <<<<<<<<<<<<<<
*
- * # map samtools code to python.struct code and byte size
+ * retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_tags, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(__pyx_int_0);
+ __pyx_r = __pyx_int_0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2269
+ /* "csamtools.pyx":2190
+ * return 0
*
- * # map samtools code to python.struct code and byte size
- * buffer = ctypes.create_string_buffer(max_size) # <<<<<<<<<<<<<<
+ * retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t)) # <<<<<<<<<<<<<<
*
- * for pytag, value in tags:
+ * if retval: return retval
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__ctypes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s_63); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyInt_FromLong(__pyx_v_max_size); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_buffer);
- __pyx_v_buffer = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_retval = memcmp((&__pyx_v_t->core), (&__pyx_v_o->core), (sizeof(bam1_core_t)));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2271
- * buffer = ctypes.create_string_buffer(max_size)
+ /* "csamtools.pyx":2192
+ * retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
*
- * for pytag, value in tags: # <<<<<<<<<<<<<<
- * t = type(value)
- * if t == types.FloatType:
+ * if retval: return retval # <<<<<<<<<<<<<<
+ * retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
+ * if retval: return retval
*/
- if (PyList_CheckExact(__pyx_v_tags) || PyTuple_CheckExact(__pyx_v_tags)) {
- __pyx_t_5 = 0; __pyx_t_1 = __pyx_v_tags; __Pyx_INCREF(__pyx_t_1);
- } else {
- __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_tags); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- }
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_1))) {
- if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_1))) {
- if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++;
- } else {
- __pyx_t_4 = PyIter_Next(__pyx_t_1);
- if (!__pyx_t_4) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_4);
- }
- if (PyTuple_CheckExact(__pyx_t_4) && likely(PyTuple_GET_SIZE(__pyx_t_4) == 2)) {
- PyObject* tuple = __pyx_t_4;
- __pyx_t_3 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_3);
- __pyx_t_6 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_pytag);
- __pyx_v_pytag = __pyx_t_3;
- __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_6;
- __pyx_t_6 = 0;
- } else {
- __pyx_t_7 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_7, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_UnpackItem(__pyx_t_7, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if (__Pyx_EndUnpack(__pyx_t_7, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_v_pytag);
- __pyx_v_pytag = __pyx_t_3;
- __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_6;
- __pyx_t_6 = 0;
- }
+ if (__pyx_v_retval) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2272
+ /* "csamtools.pyx":2193
*
- * for pytag, value in tags:
- * t = type(value) # <<<<<<<<<<<<<<
- * if t == types.FloatType:
- * fmt, pytype = "<cccf", 'f'
+ * if retval: return retval
+ * retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len) # <<<<<<<<<<<<<<
+ * if retval: return retval
+ * return memcmp(t.data, o.data, t.data_len)
*/
- __Pyx_INCREF(((PyObject *)Py_TYPE(__pyx_v_value)));
- __Pyx_DECREF(((PyObject *)__pyx_v_t));
- __pyx_v_t = ((PyObject *)((PyObject *)Py_TYPE(__pyx_v_value)));
+ __pyx_v_retval = ((__pyx_v_t->data_len > __pyx_v_o->data_len) - (__pyx_v_t->data_len < __pyx_v_o->data_len));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2273
- * for pytag, value in tags:
- * t = type(value)
- * if t == types.FloatType: # <<<<<<<<<<<<<<
- * fmt, pytype = "<cccf", 'f'
- * elif t == types.IntType:
+ /* "csamtools.pyx":2194
+ * if retval: return retval
+ * retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
+ * if retval: return retval # <<<<<<<<<<<<<<
+ * return memcmp(t.data, o.data, t.data_len)
+ *
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__types); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__FloatType); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_t), __pyx_t_6, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_2) {
+ if (__pyx_v_retval) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2274
- * t = type(value)
- * if t == types.FloatType:
- * fmt, pytype = "<cccf", 'f' # <<<<<<<<<<<<<<
- * elif t == types.IntType:
- * if value < 0:
+ /* "csamtools.pyx":2195
+ * retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
+ * if retval: return retval
+ * return memcmp(t.data, o.data, t.data_len) # <<<<<<<<<<<<<<
+ *
+ * # Disabled so long as __cmp__ is a special method
*/
- __pyx_t_4 = ((PyObject *)__pyx_kp_s_64);
- __Pyx_INCREF(__pyx_t_4);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_4;
- __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L8;
- }
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyInt_FromLong(memcmp(__pyx_v_t->data, __pyx_v_o->data, __pyx_v_t->data_len)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2275
- * if t == types.FloatType:
- * fmt, pytype = "<cccf", 'f'
- * elif t == types.IntType: # <<<<<<<<<<<<<<
- * if value < 0:
- * if value >= -127: fmt, pytype = "<cccb", 'c'
- */
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__types); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__IntType); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_RichCompare(((PyObject *)__pyx_v_t), __pyx_t_4, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_2) {
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2276
- * fmt, pytype = "<cccf", 'f'
- * elif t == types.IntType:
- * if value < 0: # <<<<<<<<<<<<<<
- * if value >= -127: fmt, pytype = "<cccb", 'c'
- * elif value >= -32767: fmt, pytype = "<ccch", 's'
- */
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_value, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_2) {
+/* Python wrapper */
+static Py_hash_t __pyx_pw_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self); /*proto*/
+static Py_hash_t __pyx_pw_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self) {
+ Py_hash_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8__hash__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2277
- * elif t == types.IntType:
- * if value < 0:
- * if value >= -127: fmt, pytype = "<cccb", 'c' # <<<<<<<<<<<<<<
- * elif value >= -32767: fmt, pytype = "<ccch", 's'
- * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+/* "csamtools.pyx":2198
+ *
+ * # Disabled so long as __cmp__ is a special method
+ * def __hash__(self): # <<<<<<<<<<<<<<
+ * return _Py_HashPointer(<void *>self)
+ *
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_2) {
- __pyx_t_6 = ((PyObject *)__pyx_kp_s_65);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_4 = ((PyObject *)__pyx_n_s__c);
- __Pyx_INCREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_6;
- __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_4;
- __pyx_t_4 = 0;
- goto __pyx_L10;
- }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2278
- * if value < 0:
- * if value >= -127: fmt, pytype = "<cccb", 'c'
- * elif value >= -32767: fmt, pytype = "<ccch", 's' # <<<<<<<<<<<<<<
- * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
- * else: fmt, pytype = "<ccci", 'i'[0]
- */
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_2) {
- __pyx_t_4 = ((PyObject *)__pyx_kp_s_66);
- __Pyx_INCREF(__pyx_t_4);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__s);
- __Pyx_INCREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_4;
- __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L10;
- }
+static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ Py_hash_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__hash__", 0);
+ __Pyx_TraceCall("__hash__", __pyx_f[0], 2198);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2279
- * if value >= -127: fmt, pytype = "<cccb", 'c'
- * elif value >= -32767: fmt, pytype = "<ccch", 's'
- * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
- * else: fmt, pytype = "<ccci", 'i'[0]
- * else:
+ /* "csamtools.pyx":2199
+ * # Disabled so long as __cmp__ is a special method
+ * def __hash__(self):
+ * return _Py_HashPointer(<void *>self) # <<<<<<<<<<<<<<
+ *
+ * property qname:
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_2) {
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_67), __pyx_v_value); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
- }
- /*else*/ {
+ __pyx_r = _Py_HashPointer(((void *)__pyx_v_self));
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2280
- * elif value >= -32767: fmt, pytype = "<ccch", 's'
- * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
- * else: fmt, pytype = "<ccci", 'i'[0] # <<<<<<<<<<<<<<
- * else:
- * if value <= 255: fmt, pytype = "<cccB", 'C'
- */
- __pyx_t_6 = ((PyObject *)__pyx_kp_s_68);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_4 = __Pyx_GetItemInt(((PyObject *)__pyx_n_s__i), 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2280; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_6;
- __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_4;
- __pyx_t_4 = 0;
- }
- __pyx_L10:;
- goto __pyx_L9;
- }
- /*else*/ {
+ __pyx_r = 0;
+ __pyx_L0:;
+ if (unlikely(__pyx_r == -1) && !PyErr_Occurred()) __pyx_r = -2;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2282
- * else: fmt, pytype = "<ccci", 'i'[0]
- * else:
- * if value <= 255: fmt, pytype = "<cccB", 'C' # <<<<<<<<<<<<<<
- * elif value <= 65535: fmt, pytype = "<cccH", 'S'
- * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
- */
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_value, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_2) {
- __pyx_t_4 = ((PyObject *)__pyx_kp_s_69);
- __Pyx_INCREF(__pyx_t_4);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__C);
- __Pyx_INCREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_4;
- __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L11;
- }
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qname___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2283
- * else:
- * if value <= 255: fmt, pytype = "<cccB", 'C'
- * elif value <= 65535: fmt, pytype = "<cccH", 'S' # <<<<<<<<<<<<<<
- * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
- * else: fmt, pytype = "<cccI", 'I'
+/* "csamtools.pyx":2203
+ * property qname:
+ * """the query name (None if not present)"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * src = self._delegate
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_value, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_2) {
- __pyx_t_6 = ((PyObject *)__pyx_kp_s_70);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_4 = ((PyObject *)__pyx_n_s__S);
- __Pyx_INCREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_6;
- __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_4;
- __pyx_t_4 = 0;
- goto __pyx_L11;
- }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2284
- * if value <= 255: fmt, pytype = "<cccB", 'C'
- * elif value <= 65535: fmt, pytype = "<cccH", 'S'
- * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
- * else: fmt, pytype = "<cccI", 'I'
- * else:
- */
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_value, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_2) {
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_67), __pyx_v_value); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
- }
- /*else*/ {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2203);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2285
- * elif value <= 65535: fmt, pytype = "<cccH", 'S'
- * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
- * else: fmt, pytype = "<cccI", 'I' # <<<<<<<<<<<<<<
- * else:
- * # Note: hex strings (H) are not supported yet
+ /* "csamtools.pyx":2205
+ * def __get__(self):
+ * cdef bam1_t * src
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.core.l_qname == 0: return None
+ * return _charptr_to_str(<char *>bam1_qname( src ))
*/
- __pyx_t_4 = ((PyObject *)__pyx_kp_s_71);
- __Pyx_INCREF(__pyx_t_4);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_4;
- __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_6;
- __pyx_t_6 = 0;
- }
- __pyx_L11:;
- }
- __pyx_L9:;
- goto __pyx_L8;
- }
- /*else*/ {
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2288
- * else:
- * # Note: hex strings (H) are not supported yet
- * if len(value) == 1: # <<<<<<<<<<<<<<
- * fmt, pytype = "<cccc", 'A'
- * else:
+ /* "csamtools.pyx":2206
+ * cdef bam1_t * src
+ * src = self._delegate
+ * if src.core.l_qname == 0: return None # <<<<<<<<<<<<<<
+ * return _charptr_to_str(<char *>bam1_qname( src ))
+ *
*/
- __pyx_t_8 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = (__pyx_t_8 == 1);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.l_qname == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2289
- * # Note: hex strings (H) are not supported yet
- * if len(value) == 1:
- * fmt, pytype = "<cccc", 'A' # <<<<<<<<<<<<<<
- * else:
- * fmt, pytype = "<ccc%is" % (len(value)+1), 'Z'
+ /* "csamtools.pyx":2207
+ * src = self._delegate
+ * if src.core.l_qname == 0: return None
+ * return _charptr_to_str(<char *>bam1_qname( src )) # <<<<<<<<<<<<<<
+ *
+ * def __set__(self, qname ):
*/
- __pyx_t_6 = ((PyObject *)__pyx_kp_s_72);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_4 = ((PyObject *)__pyx_n_s__A);
- __Pyx_INCREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_6;
- __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_4;
- __pyx_t_4 = 0;
- goto __pyx_L12;
- }
- /*else*/ {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str(((char *)bam1_qname(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2291
- * fmt, pytype = "<cccc", 'A'
- * else:
- * fmt, pytype = "<ccc%is" % (len(value)+1), 'Z' # <<<<<<<<<<<<<<
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2209
+ * return _charptr_to_str(<char *>bam1_qname( src ))
*
- * size = struct.calcsize(fmt)
+ * def __set__(self, qname ): # <<<<<<<<<<<<<<
+ * if qname == None or len(qname) == 0: return
+ * qname = _force_bytes(qname)
*/
- __pyx_t_8 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = PyInt_FromSsize_t((__pyx_t_8 + 1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_73), __pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = ((PyObject *)__pyx_n_s__Z);
- __Pyx_INCREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_v_fmt);
- __pyx_v_fmt = ((PyObject *)__pyx_t_6);
- __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_4;
- __pyx_t_4 = 0;
- }
- __pyx_L12:;
- }
- __pyx_L8:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2293
- * fmt, pytype = "<ccc%is" % (len(value)+1), 'Z'
+static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname) {
+ bam1_t *__pyx_v_src;
+ int __pyx_v_l;
+ char *__pyx_v_p;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ Py_ssize_t __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ char *__pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2209);
+ __Pyx_INCREF(__pyx_v_qname);
+
+ /* "csamtools.pyx":2210
*
- * size = struct.calcsize(fmt) # <<<<<<<<<<<<<<
- * if offset + size > max_size:
- * raise NotImplementedError("tags field too large")
+ * def __set__(self, qname ):
+ * if qname == None or len(qname) == 0: return # <<<<<<<<<<<<<<
+ * qname = _force_bytes(qname)
+ * cdef bam1_t * src
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__calcsize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_v_fmt);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_fmt);
- __Pyx_GIVEREF(__pyx_v_fmt);
- __pyx_t_3 = PyObject_Call(__pyx_t_6, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_size = __pyx_t_9;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!__pyx_t_2) {
+ __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__pyx_t_3 == 0);
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_2;
+ }
+ if (__pyx_t_5) {
+ __pyx_r = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2211
+ * def __set__(self, qname ):
+ * if qname == None or len(qname) == 0: return
+ * qname = _force_bytes(qname) # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * cdef int l
+ */
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_qname)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_v_qname);
+ __pyx_v_qname = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2294
+ /* "csamtools.pyx":2216
+ * cdef char * p
*
- * size = struct.calcsize(fmt)
- * if offset + size > max_size: # <<<<<<<<<<<<<<
- * raise NotImplementedError("tags field too large")
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * p = bam1_qname( src )
*
*/
- __pyx_t_2 = ((__pyx_v_offset + __pyx_v_size) > __pyx_v_max_size);
- if (__pyx_t_2) {
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2295
- * size = struct.calcsize(fmt)
- * if offset + size > max_size:
- * raise NotImplementedError("tags field too large") # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2217
+ *
+ * src = self._delegate
+ * p = bam1_qname( src ) # <<<<<<<<<<<<<<
*
- * struct.pack_into( fmt,
+ * # the qname is \0 terminated
*/
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_74));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_kp_s_74));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_74));
- __pyx_t_4 = PyObject_Call(__pyx_builtin_NotImplementedError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L13;
- }
- __pyx_L13:;
+ __pyx_v_p = bam1_qname(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2297
- * raise NotImplementedError("tags field too large")
+ /* "csamtools.pyx":2220
*
- * struct.pack_into( fmt, # <<<<<<<<<<<<<<
- * buffer,
- * offset,
+ * # the qname is \0 terminated
+ * l = len(qname) + 1 # <<<<<<<<<<<<<<
+ * pysam_bam_update( src,
+ * src.core.l_qname,
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__pack_into); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_l = (__pyx_t_3 + 1);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2299
- * struct.pack_into( fmt,
- * buffer,
- * offset, # <<<<<<<<<<<<<<
- * pytag[0],
- * pytag[1],
+ /* "csamtools.pyx":2224
+ * src.core.l_qname,
+ * l,
+ * <uint8_t*>p ) # <<<<<<<<<<<<<<
+ *
+ * src.core.l_qname = l
*/
- __pyx_t_4 = PyInt_FromLong(__pyx_v_offset); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ pysam_bam_update(__pyx_v_src, __pyx_v_src->core.l_qname, __pyx_v_l, ((uint8_t *)__pyx_v_p));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2300
- * buffer,
- * offset,
- * pytag[0], # <<<<<<<<<<<<<<
- * pytag[1],
- * pytype,
+ /* "csamtools.pyx":2226
+ * <uint8_t*>p )
+ *
+ * src.core.l_qname = l # <<<<<<<<<<<<<<
+ *
+ * # re-acquire pointer to location in memory
*/
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_pytag, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_v_src->core.l_qname = __pyx_v_l;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2301
- * offset,
- * pytag[0],
- * pytag[1], # <<<<<<<<<<<<<<
- * pytype,
- * value )
+ /* "csamtools.pyx":2230
+ * # re-acquire pointer to location in memory
+ * # as it might have moved
+ * p = bam1_qname(src) # <<<<<<<<<<<<<<
+ *
+ * strncpy( p, qname, l )
*/
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_pytag, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_v_p = bam1_qname(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2303
- * pytag[1],
- * pytype,
- * value ) # <<<<<<<<<<<<<<
- * offset += size
+ /* "csamtools.pyx":2232
+ * p = bam1_qname(src)
+ *
+ * strncpy( p, qname, l ) # <<<<<<<<<<<<<<
*
+ * property cigar:
*/
- __pyx_t_10 = PyTuple_New(7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_INCREF(__pyx_v_fmt);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_fmt);
- __Pyx_GIVEREF(__pyx_v_fmt);
- __Pyx_INCREF(__pyx_v_buffer);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_buffer);
- __Pyx_GIVEREF(__pyx_v_buffer);
- PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_10, 4, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __Pyx_INCREF(__pyx_v_pytype);
- PyTuple_SET_ITEM(__pyx_t_10, 5, __pyx_v_pytype);
- __Pyx_GIVEREF(__pyx_v_pytype);
- __Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_10, 6, __pyx_v_value);
- __Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_4 = 0;
- __pyx_t_6 = 0;
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_3, __pyx_t_10, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_6 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy(__pyx_v_p, __pyx_t_6, __pyx_v_l);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2304
- * pytype,
- * value )
- * offset += size # <<<<<<<<<<<<<<
- *
- * # delete the old data and allocate new
- */
- __pyx_v_offset += __pyx_v_size;
- }
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_qname);
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2312
- * src.l_aux,
- * offset,
- * bam1_aux( src ) ) # <<<<<<<<<<<<<<
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2259
*
- * src.l_aux = offset
+ * """
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef uint32_t * cigar_p
+ * cdef bam1_t * src
*/
- pysam_bam_update(__pyx_v_src, __pyx_v_src->l_aux, __pyx_v_offset, bam1_aux(__pyx_v_src));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2314
- * bam1_aux( src ) )
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_op = 0;
+ PyObject *__pyx_v_l = 0;
+ PyObject *__pyx_v_cigar = 0;
+ int __pyx_v_k;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ uint32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2259);
+
+ /* "csamtools.pyx":2265
+ * cdef int k
*
- * src.l_aux = offset # <<<<<<<<<<<<<<
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.core.n_cigar == 0: return None
*
- * # copy data only if there is any
*/
- __pyx_v_src->l_aux = __pyx_v_offset;
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2317
+ /* "csamtools.pyx":2266
*
- * # copy data only if there is any
- * if offset != 0: # <<<<<<<<<<<<<<
+ * src = self._delegate
+ * if src.core.n_cigar == 0: return None # <<<<<<<<<<<<<<
*
- * # get location of new data
+ * cigar = []
*/
- __pyx_t_2 = (__pyx_v_offset != 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2320
- *
- * # get location of new data
- * s = bam1_aux( src ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2268
+ * if src.core.n_cigar == 0: return None
*
- * # check if there is direct path from buffer.raw to tmp
+ * cigar = [] # <<<<<<<<<<<<<<
+ * cigar_p = bam1_cigar(src);
+ * for k from 0 <= k < src.core.n_cigar:
*/
- __pyx_v_s = bam1_aux(__pyx_v_src);
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_cigar = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2323
- *
- * # check if there is direct path from buffer.raw to tmp
- * temp = buffer.raw # <<<<<<<<<<<<<<
- * memcpy( s, temp, offset )
+ /* "csamtools.pyx":2269
*
+ * cigar = []
+ * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = PyBytes_AsString(__pyx_t_1); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_v_temp = __pyx_t_11;
+ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2324
- * # check if there is direct path from buffer.raw to tmp
- * temp = buffer.raw
- * memcpy( s, temp, offset ) # <<<<<<<<<<<<<<
- *
- * property flag:
+ /* "csamtools.pyx":2270
+ * cigar = []
+ * cigar_p = bam1_cigar(src);
+ * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- memcpy(__pyx_v_s, __pyx_v_temp, __pyx_v_offset);
- goto __pyx_L14;
- }
- __pyx_L14:;
+ __pyx_t_3 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.AlignedRead.tags.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_buffer);
- __Pyx_DECREF(__pyx_v_pytag);
- __Pyx_DECREF(__pyx_v_value);
- __Pyx_DECREF(__pyx_v_t);
- __Pyx_DECREF(__pyx_v_fmt);
- __Pyx_DECREF(__pyx_v_pytype);
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2271
+ * cigar_p = bam1_cigar(src);
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * cigar.append((op, l))
+ */
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_op);
+ __pyx_v_op = __pyx_t_2;
+ __pyx_t_2 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2328
- * property flag:
- * """properties flag"""
- * def __get__(self): return self._delegate.core.flag # <<<<<<<<<<<<<<
- * def __set__(self, flag): self._delegate.core.flag = flag
+ /* "csamtools.pyx":2272
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
+ * cigar.append((op, l))
+ * return cigar
+ */
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_l);
+ __pyx_v_l = __pyx_t_2;
+ __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":2273
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * cigar.append((op, l)) # <<<<<<<<<<<<<<
+ * return cigar
*
*/
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_op);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op);
+ __Pyx_GIVEREF(__pyx_v_op);
+ __Pyx_INCREF(__pyx_v_l);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_l);
+ __Pyx_GIVEREF(__pyx_v_l);
+ __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ }
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2328);
+ /* "csamtools.pyx":2274
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * cigar.append((op, l))
+ * return cigar # <<<<<<<<<<<<<<
+ *
+ * def __set__(self, values ):
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __Pyx_INCREF(__pyx_v_cigar);
+ __pyx_r = __pyx_v_cigar;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.flag.__get__");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_op);
+ __Pyx_XDECREF(__pyx_v_l);
+ __Pyx_XDECREF(__pyx_v_cigar);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2329
- * """properties flag"""
- * def __get__(self): return self._delegate.core.flag
- * def __set__(self, flag): self._delegate.core.flag = flag # <<<<<<<<<<<<<<
- *
- * property rname:
- */
-
-static int __pyx_pf_9csamtools_11AlignedRead_4flag___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4flag___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
int __pyx_r;
- uint32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2329);
- __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_flag); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = __pyx_t_1;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.flag.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_values));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2347
- *
- * """
- * def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
- * def __set__(self, tid): self._delegate.core.tid = tid
+/* "csamtools.pyx":2276
+ * return cigar
*
+ * def __set__(self, values ): # <<<<<<<<<<<<<<
+ * if values == None or len(values) == 0: return
+ * cdef uint32_t * p
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values) {
+ uint32_t *__pyx_v_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_op = 0;
+ PyObject *__pyx_v_l = 0;
+ int __pyx_v_k;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ Py_ssize_t __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ uint32_t __pyx_t_12;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2347);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2276);
+
+ /* "csamtools.pyx":2277
+ *
+ * def __set__(self, values ):
+ * if values == None or len(values) == 0: return # <<<<<<<<<<<<<<
+ * cdef uint32_t * p
+ * cdef bam1_t * src
+ */
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!__pyx_t_2) {
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__pyx_t_3 == 0);
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_2;
+ }
+ if (__pyx_t_5) {
+ __pyx_r = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.rname.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2283
+ * cdef int k
+ *
+ * k = 0 # <<<<<<<<<<<<<<
+ *
+ * src = self._delegate
+ */
+ __pyx_v_k = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2348
- * """
- * def __get__(self): return self._delegate.core.tid
- * def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2285
+ * k = 0
*
- * property tid:
+ * src = self._delegate # <<<<<<<<<<<<<<
+ *
+ * # get location of cigar string
*/
+ __pyx_v_src = __pyx_v_self->_delegate;
-static int __pyx_pf_9csamtools_11AlignedRead_5rname___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rname___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- int __pyx_r;
- int32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2348);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
+ /* "csamtools.pyx":2288
+ *
+ * # get location of cigar string
+ * p = bam1_cigar(src) # <<<<<<<<<<<<<<
+ *
+ * # create space for cigar data within src.data
+ */
+ __pyx_v_p = bam1_cigar(__pyx_v_src);
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.rname.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2293
+ * pysam_bam_update( src,
+ * src.core.n_cigar * 4,
+ * len(values) * 4, # <<<<<<<<<<<<<<
+ * <uint8_t*>p )
+ *
+ */
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2361
+ /* "csamtools.pyx":2294
+ * src.core.n_cigar * 4,
+ * len(values) * 4,
+ * <uint8_t*>p ) # <<<<<<<<<<<<<<
*
- * """
- * def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
- * def __set__(self, tid): self._delegate.core.tid = tid
+ * # length is number of cigar operations, not bytes
+ */
+ pysam_bam_update(__pyx_v_src, (__pyx_v_src->core.n_cigar * 4), (__pyx_t_3 * 4), ((uint8_t *)__pyx_v_p));
+
+ /* "csamtools.pyx":2297
+ *
+ * # length is number of cigar operations, not bytes
+ * src.core.n_cigar = len(values) # <<<<<<<<<<<<<<
*
+ * # re-acquire pointer to location in memory
*/
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_src->core.n_cigar = __pyx_t_3;
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2361);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ /* "csamtools.pyx":2301
+ * # re-acquire pointer to location in memory
+ * # as it might have moved
+ * p = bam1_cigar(src) # <<<<<<<<<<<<<<
+ *
+ * # insert cigar operations
+ */
+ __pyx_v_p = bam1_cigar(__pyx_v_src);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.tid.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2304
+ *
+ * # insert cigar operations
+ * for op, l in values: # <<<<<<<<<<<<<<
+ * p[k] = l << BAM_CIGAR_SHIFT | op
+ * k += 1
+ */
+ if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
+ __pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ }
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else {
+ __pyx_t_7 = __pyx_t_6(__pyx_t_1);
+ if (unlikely(!__pyx_t_7)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_7);
+ }
+ if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
+ PyObject* sequence = __pyx_t_7;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_8);
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_op);
+ __pyx_v_op = __pyx_t_8;
+ __pyx_t_8 = 0;
+ __Pyx_XDECREF(__pyx_v_l);
+ __pyx_v_l = __pyx_t_9;
+ __pyx_t_9 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2362
- * """
- * def __get__(self): return self._delegate.core.tid
- * def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2305
+ * # insert cigar operations
+ * for op, l in values:
+ * p[k] = l << BAM_CIGAR_SHIFT | op # <<<<<<<<<<<<<<
+ * k += 1
*
- * property pos:
*/
+ __pyx_t_7 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = PyNumber_Or(__pyx_t_7, __pyx_v_op); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_12 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ (__pyx_v_p[__pyx_v_k]) = __pyx_t_12;
-static int __pyx_pf_9csamtools_11AlignedRead_3tid___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3tid___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- int __pyx_r;
- int32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2362);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
+ /* "csamtools.pyx":2306
+ * for op, l in values:
+ * p[k] = l << BAM_CIGAR_SHIFT | op
+ * k += 1 # <<<<<<<<<<<<<<
+ *
+ * ## setting the cigar string also updates the "bin" attribute
+ */
+ __pyx_v_k = (__pyx_v_k + 1);
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2309
+ *
+ * ## setting the cigar string also updates the "bin" attribute
+ * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, p)) # <<<<<<<<<<<<<<
+ *
+ * property cigarstring:
+ */
+ __pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), __pyx_v_p));
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.tid.__set__");
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_op);
+ __Pyx_XDECREF(__pyx_v_l);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2366
- * property pos:
- * """0-based leftmost coordinate"""
- * def __get__(self): return self._delegate.core.pos # <<<<<<<<<<<<<<
- * def __set__(self, pos):
- * ## setting the cigar string also updates the "bin" attribute
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2316
+ * Returns the empty string if not present.
+ * '''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * c = self.cigar
+ * if c == None: return ""
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_v_c = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_y = NULL;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ Py_ssize_t __pyx_t_12;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2366);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2316);
+
+ /* "csamtools.pyx":2317
+ * '''
+ * def __get__(self):
+ * c = self.cigar # <<<<<<<<<<<<<<
+ * if c == None: return ""
+ * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
+ */
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
+ __pyx_v_c = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L0;
+
+ /* "csamtools.pyx":2318
+ * def __get__(self):
+ * c = self.cigar
+ * if c == None: return "" # <<<<<<<<<<<<<<
+ * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
+ *
+ */
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_c, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_16));
+ __pyx_r = ((PyObject *)__pyx_kp_s_16);
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2319
+ * c = self.cigar
+ * if c == None: return ""
+ * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c]) # <<<<<<<<<<<<<<
+ *
+ * def __set__(self, cigar):
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (PyList_CheckExact(__pyx_v_c) || PyTuple_CheckExact(__pyx_v_c)) {
+ __pyx_t_4 = __pyx_v_c; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_c); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext;
+ }
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
+ } else {
+ __pyx_t_7 = __pyx_t_6(__pyx_t_4);
+ if (unlikely(!__pyx_t_7)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_7);
+ }
+ if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
+ PyObject* sequence = __pyx_t_7;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_8);
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
+ __Pyx_XDECREF(__pyx_v_y);
+ __pyx_v_y = __pyx_t_9;
+ __pyx_t_9 = 0;
+ __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromLong((__pyx_v_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_y);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_y);
+ __Pyx_GIVEREF(__pyx_v_y);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_135), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_INCREF(((PyObject *)__pyx_t_3));
+ PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
+ goto __pyx_L0;
+ }
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.pos.__get__");
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigarstring.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_c);
+ __Pyx_XDECREF(__pyx_v_x);
+ __Pyx_XDECREF(__pyx_v_y);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2367
- * """0-based leftmost coordinate"""
- * def __get__(self): return self._delegate.core.pos
- * def __set__(self, pos): # <<<<<<<<<<<<<<
- * ## setting the cigar string also updates the "bin" attribute
- * cdef bam1_t * src
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_cigar));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2321
+ * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
+ *
+ * def __set__(self, cigar): # <<<<<<<<<<<<<<
+ * if cigar == None or len(cigar) == 0: self.cigar = []
+ * parts = CIGAR_REGEX.findall( cigar )
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3pos___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3pos___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
- bam1_t *__pyx_v_src;
+static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar) {
+ PyObject *__pyx_v_parts = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_y = NULL;
int __pyx_r;
- int32_t __pyx_t_1;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ Py_ssize_t __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *(*__pyx_t_8)(PyObject *);
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ PyObject *(*__pyx_t_12)(PyObject *);
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2367);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2321);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2370
- * ## setting the cigar string also updates the "bin" attribute
- * cdef bam1_t * src
- * src = self._delegate # <<<<<<<<<<<<<<
- * if src.core.n_cigar:
- * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
+ /* "csamtools.pyx":2322
+ *
+ * def __set__(self, cigar):
+ * if cigar == None or len(cigar) == 0: self.cigar = [] # <<<<<<<<<<<<<<
+ * parts = CIGAR_REGEX.findall( cigar )
+ * self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ]
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2371
- * cdef bam1_t * src
- * src = self._delegate
- * if src.core.n_cigar: # <<<<<<<<<<<<<<
- * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
- * else:
- */
- if (__pyx_v_src->core.n_cigar) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2372
- * src = self._delegate
- * if src.core.n_cigar:
- * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) ) # <<<<<<<<<<<<<<
- * else:
- * src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
- */
- __pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)));
- goto __pyx_L5;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_cigar, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!__pyx_t_2) {
+ __pyx_t_3 = PyObject_Length(__pyx_v_cigar); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__pyx_t_3 == 0);
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_2;
}
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2374
- * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
- * else:
- * src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1) # <<<<<<<<<<<<<<
- * self._delegate.core.pos = pos
- * property bin:
- */
- __pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, (__pyx_v_src->core.pos + 1));
+ if (__pyx_t_5) {
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ goto __pyx_L3;
}
- __pyx_L5:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2375
- * else:
- * src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
- * self._delegate.core.pos = pos # <<<<<<<<<<<<<<
- * property bin:
- * """properties bin"""
- */
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos = __pyx_t_1;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.pos.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_L3:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2378
- * property bin:
- * """properties bin"""
- * def __get__(self): return self._delegate.core.bin # <<<<<<<<<<<<<<
- * def __set__(self, bin): self._delegate.core.bin = bin
- * property rlen:
+ /* "csamtools.pyx":2323
+ * def __set__(self, cigar):
+ * if cigar == None or len(cigar) == 0: self.cigar = []
+ * parts = CIGAR_REGEX.findall( cigar ) # <<<<<<<<<<<<<<
+ * self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ]
+ *
*/
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2378);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR_REGEX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.bin.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__findall); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_cigar);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_cigar);
+ __Pyx_GIVEREF(__pyx_v_cigar);
+ __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_v_parts = __pyx_t_7;
+ __pyx_t_7 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2379
- * """properties bin"""
- * def __get__(self): return self._delegate.core.bin
- * def __set__(self, bin): self._delegate.core.bin = bin # <<<<<<<<<<<<<<
- * property rlen:
- * '''length of the read (read only). Returns 0 if not given.'''
+ /* "csamtools.pyx":2324
+ * if cigar == None or len(cigar) == 0: self.cigar = []
+ * parts = CIGAR_REGEX.findall( cigar )
+ * self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ] # <<<<<<<<<<<<<<
+ *
+ * property seq:
*/
-
-static int __pyx_pf_9csamtools_11AlignedRead_3bin___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3bin___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
- int __pyx_r;
- uint32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2379);
- __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_bin); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin = __pyx_t_1;
+ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyList_CheckExact(__pyx_v_parts) || PyTuple_CheckExact(__pyx_v_parts)) {
+ __pyx_t_1 = __pyx_v_parts; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
+ __pyx_t_8 = NULL;
+ } else {
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_parts); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ }
+ for (;;) {
+ if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ } else {
+ __pyx_t_6 = __pyx_t_8(__pyx_t_1);
+ if (unlikely(!__pyx_t_6)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_6);
+ }
+ if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
+ PyObject* sequence = __pyx_t_6;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_11 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
+ index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_10);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_x);
+ __pyx_v_x = __pyx_t_9;
+ __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_v_y);
+ __pyx_v_y = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR2CODE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_INCREF(__pyx_v_x);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_x);
+ __Pyx_GIVEREF(__pyx_v_x);
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ord, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_GetItem(__pyx_t_6, __pyx_t_9); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_v_y);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_y);
+ __Pyx_GIVEREF(__pyx_v_y);
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_10 = 0;
+ __pyx_t_6 = 0;
+ if (unlikely(PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_9))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.bin.__set__");
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigarstring.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_parts);
+ __Pyx_XDECREF(__pyx_v_x);
+ __Pyx_XDECREF(__pyx_v_y);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2382
- * property rlen:
- * '''length of the read (read only). Returns 0 if not given.'''
- * def __get__(self): return self._delegate.core.l_qseq # <<<<<<<<<<<<<<
- * property aend:
- * '''aligned end position of the read (read only). Returns
- */
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2382);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.rlen.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3seq___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2386
- * '''aligned end position of the read (read only). Returns
- * None if not available.'''
+/* "csamtools.pyx":2330
+ *
+ * In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
* def __get__(self): # <<<<<<<<<<<<<<
* cdef bam1_t * src
- * src = self._delegate
+ * cdef char * s
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2386);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2330);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2388
- * def __get__(self):
+ /* "csamtools.pyx":2333
* cdef bam1_t * src
+ * cdef char * s
* src = self._delegate # <<<<<<<<<<<<<<
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
- * return None
- */
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2389
- * cdef bam1_t * src
- * src = self._delegate
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
- * return None
- * return bam_calend(&src.core, bam1_cigar(src))
+ *
+ * if src.core.l_qseq == 0: return None
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!__pyx_t_3) {
- __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
- __pyx_t_5 = __pyx_t_4;
- } else {
- __pyx_t_5 = __pyx_t_3;
- }
- if (__pyx_t_5) {
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2390
+ /* "csamtools.pyx":2335
* src = self._delegate
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
- * return None # <<<<<<<<<<<<<<
- * return bam_calend(&src.core, bam1_cigar(src))
- * property alen:
+ *
+ * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ *
+ * return get_seq_range(src, 0, src.core.l_qseq)
*/
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2391
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
- * return None
- * return bam_calend(&src.core, bam1_cigar(src)) # <<<<<<<<<<<<<<
- * property alen:
- * '''aligned length of the read (read only). Returns None if
+ /* "csamtools.pyx":2337
+ * if src.core.l_qseq == 0: return None
+ *
+ * return get_seq_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
+ *
+ * def __set__(self,seq):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.aend.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.seq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2395
- * '''aligned length of the read (read only). Returns None if
- * not available.'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef bam1_t * src
- * src = self._delegate
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_seq));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2339
+ * return get_seq_range(src, 0, src.core.l_qseq)
+ *
+ * def __set__(self,seq): # <<<<<<<<<<<<<<
+ * # samtools manages sequence and quality length memory together
+ * # if no quality information is present, the first byte says 0xff.
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self) {
+static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq) {
bam1_t *__pyx_v_src;
- PyObject *__pyx_r = NULL;
+ uint8_t *__pyx_v_p;
+ char *__pyx_v_s;
+ int __pyx_v_l;
+ int __pyx_v_k;
+ int __pyx_v_nbytes_new;
+ int __pyx_v_nbytes_old;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ int __pyx_t_2;
+ Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
+ int __pyx_t_6;
+ char *__pyx_t_7;
+ long __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2395);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2339);
+ __Pyx_INCREF(__pyx_v_seq);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2397
- * def __get__(self):
+ /* "csamtools.pyx":2343
+ * # if no quality information is present, the first byte says 0xff.
+ *
+ * if seq == None or len(seq) == 0: return # <<<<<<<<<<<<<<
+ * seq = _force_bytes(seq)
* cdef bam1_t * src
- * src = self._delegate # <<<<<<<<<<<<<<
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
- * return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2398
- * cdef bam1_t * src
- * src = self._delegate
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
- * return None
- * return bam_calend(&src.core,
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!__pyx_t_3) {
- __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
+ if (!__pyx_t_2) {
+ __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
} else {
- __pyx_t_5 = __pyx_t_3;
+ __pyx_t_5 = __pyx_t_2;
}
if (__pyx_t_5) {
+ __pyx_r = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2344
+ *
+ * if seq == None or len(seq) == 0: return
+ * seq = _force_bytes(seq) # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * cdef uint8_t * p
+ */
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_seq)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_v_seq);
+ __pyx_v_seq = __pyx_t_1;
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2350
+ * cdef int l, k, nbytes_new, nbytes_old
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ *
+ * l = len(seq)
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2399
+ /* "csamtools.pyx":2352
* src = self._delegate
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
- * return None # <<<<<<<<<<<<<<
- * return bam_calend(&src.core,
- * bam1_cigar(src)) - \
+ *
+ * l = len(seq) # <<<<<<<<<<<<<<
+ *
+ * # as the sequence is stored in half-bytes, the total length (sequence
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_l = __pyx_t_3;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2400
- * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
- * return None
- * return bam_calend(&src.core, # <<<<<<<<<<<<<<
- * bam1_cigar(src)) - \
- * self._delegate.core.pos
+ /* "csamtools.pyx":2356
+ * # as the sequence is stored in half-bytes, the total length (sequence
+ * # plus quality scores) is (l+1)/2 + l
+ * nbytes_new = (l+1)/2 + l # <<<<<<<<<<<<<<
+ * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
+ * # acquire pointer to location in memory
*/
- __Pyx_XDECREF(__pyx_r);
+ __pyx_v_nbytes_new = (__Pyx_div_long((__pyx_v_l + 1), 2) + __pyx_v_l);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2402
- * return bam_calend(&src.core,
- * bam1_cigar(src)) - \
- * self._delegate.core.pos # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2357
+ * # plus quality scores) is (l+1)/2 + l
+ * nbytes_new = (l+1)/2 + l
+ * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq # <<<<<<<<<<<<<<
+ * # acquire pointer to location in memory
+ * p = bam1_seq( src )
+ */
+ __pyx_v_nbytes_old = (__Pyx_div_long((__pyx_v_src->core.l_qseq + 1), 2) + __pyx_v_src->core.l_qseq);
+
+ /* "csamtools.pyx":2359
+ * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
+ * # acquire pointer to location in memory
+ * p = bam1_seq( src ) # <<<<<<<<<<<<<<
+ * src.core.l_qseq = l
*
- * property mapq:
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
+ __pyx_v_p = bam1_seq(__pyx_v_src);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.alen.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2360
+ * # acquire pointer to location in memory
+ * p = bam1_seq( src )
+ * src.core.l_qseq = l # <<<<<<<<<<<<<<
+ *
+ * pysam_bam_update( src,
+ */
+ __pyx_v_src->core.l_qseq = __pyx_v_l;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2406
- * property mapq:
- * """mapping quality"""
- * def __get__(self): return self._delegate.core.qual # <<<<<<<<<<<<<<
- * def __set__(self, qual): self._delegate.core.qual = qual
- * property mrnm:
+ /* "csamtools.pyx":2365
+ * nbytes_old,
+ * nbytes_new,
+ * p) # <<<<<<<<<<<<<<
+ * # re-acquire pointer to location in memory
+ * # as it might have moved
*/
+ pysam_bam_update(__pyx_v_src, __pyx_v_nbytes_old, __pyx_v_nbytes_new, __pyx_v_p);
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2406);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2406; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ /* "csamtools.pyx":2368
+ * # re-acquire pointer to location in memory
+ * # as it might have moved
+ * p = bam1_seq( src ) # <<<<<<<<<<<<<<
+ * for k from 0 <= k < nbytes_new: p[k] = 0
+ * # convert to C string
+ */
+ __pyx_v_p = bam1_seq(__pyx_v_src);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2369
+ * # as it might have moved
+ * p = bam1_seq( src )
+ * for k from 0 <= k < nbytes_new: p[k] = 0 # <<<<<<<<<<<<<<
+ * # convert to C string
+ * s = seq
+ */
+ __pyx_t_6 = __pyx_v_nbytes_new;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
+ (__pyx_v_p[__pyx_v_k]) = 0;
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2407
- * """mapping quality"""
- * def __get__(self): return self._delegate.core.qual
- * def __set__(self, qual): self._delegate.core.qual = qual # <<<<<<<<<<<<<<
- * property mrnm:
- * """the :term:`reference` id of the mate """
+ /* "csamtools.pyx":2371
+ * for k from 0 <= k < nbytes_new: p[k] = 0
+ * # convert to C string
+ * s = seq # <<<<<<<<<<<<<<
+ * for k from 0 <= k < l:
+ * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
*/
+ __pyx_t_7 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = __pyx_t_7;
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
- int __pyx_r;
- uint32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2407);
- __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual = __pyx_t_1;
+ /* "csamtools.pyx":2372
+ * # convert to C string
+ * s = seq
+ * for k from 0 <= k < l: # <<<<<<<<<<<<<<
+ * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
+ *
+ */
+ __pyx_t_6 = __pyx_v_l;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
+
+ /* "csamtools.pyx":2373
+ * s = seq
+ * for k from 0 <= k < l:
+ * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) # <<<<<<<<<<<<<<
+ *
+ * # erase qualities
+ */
+ __pyx_t_8 = __Pyx_div_long(__pyx_v_k, 2);
+ (__pyx_v_p[__pyx_t_8]) = ((__pyx_v_p[__pyx_t_8]) | (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))));
+ }
+
+ /* "csamtools.pyx":2376
+ *
+ * # erase qualities
+ * p = bam1_qual( src ) # <<<<<<<<<<<<<<
+ * p[0] = 0xff
+ *
+ */
+ __pyx_v_p = bam1_qual(__pyx_v_src);
+
+ /* "csamtools.pyx":2377
+ * # erase qualities
+ * p = bam1_qual( src )
+ * p[0] = 0xff # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ (__pyx_v_p[0]) = 0xff;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__set__");
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.AlignedRead.seq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_seq);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2410
- * property mrnm:
- * """the :term:`reference` id of the mate """
- * def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
- * def __set__(self, mtid): self._delegate.core.mtid = mtid
- * property mpos:
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qual___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2384
+ *
+ * In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ *
+ * cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2410);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2384);
+
+ /* "csamtools.pyx":2389
+ * cdef char * q
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ *
+ * if src.core.l_qseq == 0: return None
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
+
+ /* "csamtools.pyx":2391
+ * src = self._delegate
+ *
+ * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ *
+ * return get_qual_range(src, 0, src.core.l_qseq)
+ */
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2393
+ * if src.core.l_qseq == 0: return None
+ *
+ * return get_qual_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
+ *
+ * def __set__(self,qual):
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_2 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__get__");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2411
- * """the :term:`reference` id of the mate """
- * def __get__(self): return self._delegate.core.mtid
- * def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
- * property mpos:
- * """the position of the mate"""
- */
-
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
int __pyx_r;
- int32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2411);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2414
- * property mpos:
- * """the position of the mate"""
- * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
- * def __set__(self, mpos): self._delegate.core.mpos = mpos
- * property isize:
+/* "csamtools.pyx":2395
+ * return get_qual_range(src, 0, src.core.l_qseq)
+ *
+ * def __set__(self,qual): # <<<<<<<<<<<<<<
+ * # note that space is already allocated via the sequences
+ * cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
+ bam1_t *__pyx_v_src;
+ uint8_t *__pyx_v_p;
+ char *__pyx_v_q;
+ int __pyx_v_k;
+ int __pyx_v_l;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ Py_ssize_t __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ char *__pyx_t_6;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_9;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2414);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2395);
+ __Pyx_INCREF(__pyx_v_qual);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2402
+ * cdef int k
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * p = bam1_qual( src )
+ * if qual == None or len(qual) == 0:
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2415
- * """the position of the mate"""
- * def __get__(self): return self._delegate.core.mpos
- * def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
- * property isize:
- * """the insert size"""
+ /* "csamtools.pyx":2403
+ *
+ * src = self._delegate
+ * p = bam1_qual( src ) # <<<<<<<<<<<<<<
+ * if qual == None or len(qual) == 0:
+ * # if absent - set to 0xff
*/
+ __pyx_v_p = bam1_qual(__pyx_v_src);
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
- int __pyx_r;
- int32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2415);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
+ /* "csamtools.pyx":2404
+ * src = self._delegate
+ * p = bam1_qual( src )
+ * if qual == None or len(qual) == 0: # <<<<<<<<<<<<<<
+ * # if absent - set to 0xff
+ * p[0] = 0xff
+ */
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!__pyx_t_2) {
+ __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__pyx_t_3 == 0);
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_2;
+ }
+ if (__pyx_t_5) {
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2406
+ * if qual == None or len(qual) == 0:
+ * # if absent - set to 0xff
+ * p[0] = 0xff # <<<<<<<<<<<<<<
+ * return
+ * qual = _force_bytes(qual)
+ */
+ (__pyx_v_p[0]) = 0xff;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2418
- * property isize:
- * """the insert size"""
- * def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
- * def __set__(self, isize): self._delegate.core.isize = isize
- * property is_paired:
+ /* "csamtools.pyx":2407
+ * # if absent - set to 0xff
+ * p[0] = 0xff
+ * return # <<<<<<<<<<<<<<
+ * qual = _force_bytes(qual)
+ * cdef int l
*/
+ __pyx_r = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2418);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /* "csamtools.pyx":2408
+ * p[0] = 0xff
+ * return
+ * qual = _force_bytes(qual) # <<<<<<<<<<<<<<
+ * cdef int l
+ * # convert to C string
+ */
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_qual)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
+ __Pyx_DECREF(__pyx_v_qual);
+ __pyx_v_qual = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.isize.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2411
+ * cdef int l
+ * # convert to C string
+ * q = qual # <<<<<<<<<<<<<<
+ * l = len(qual)
+ * if src.core.l_qseq != l:
+ */
+ __pyx_t_6 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_q = __pyx_t_6;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2419
- * """the insert size"""
- * def __get__(self): return self._delegate.core.isize
- * def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
- * property is_paired:
- * """true if read is paired in sequencing"""
+ /* "csamtools.pyx":2412
+ * # convert to C string
+ * q = qual
+ * l = len(qual) # <<<<<<<<<<<<<<
+ * if src.core.l_qseq != l:
+ * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
*/
+ __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_l = __pyx_t_3;
-static int __pyx_pf_9csamtools_11AlignedRead_5isize___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5isize___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
- int __pyx_r;
- int32_t __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2419);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
+ /* "csamtools.pyx":2413
+ * q = qual
+ * l = len(qual)
+ * if src.core.l_qseq != l: # <<<<<<<<<<<<<<
+ * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
+ * assert src.core.l_qseq == l
+ */
+ __pyx_t_5 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
+ if (__pyx_t_5) {
+
+ /* "csamtools.pyx":2414
+ * l = len(qual)
+ * if src.core.l_qseq != l:
+ * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) # <<<<<<<<<<<<<<
+ * assert src.core.l_qseq == l
+ * for k from 0 <= k < l:
+ */
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_1 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_136), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+
+ /* "csamtools.pyx":2415
+ * if src.core.l_qseq != l:
+ * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
+ * assert src.core.l_qseq == l # <<<<<<<<<<<<<<
+ * for k from 0 <= k < l:
+ * p[k] = <uint8_t>q[k] - 33
+ */
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!(__pyx_v_src->core.l_qseq == __pyx_v_l))) {
+ PyErr_SetNone(PyExc_AssertionError);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
+
+ /* "csamtools.pyx":2416
+ * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
+ * assert src.core.l_qseq == l
+ * for k from 0 <= k < l: # <<<<<<<<<<<<<<
+ * p[k] = <uint8_t>q[k] - 33
+ *
+ */
+ __pyx_t_9 = __pyx_v_l;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_9; __pyx_v_k++) {
+
+ /* "csamtools.pyx":2417
+ * assert src.core.l_qseq == l
+ * for k from 0 <= k < l:
+ * p[k] = <uint8_t>q[k] - 33 # <<<<<<<<<<<<<<
+ *
+ * property query:
+ */
+ (__pyx_v_p[__pyx_v_k]) = (((uint8_t)(__pyx_v_q[__pyx_v_k])) - 33);
+ }
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.isize.__set__");
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qual.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_qual);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2422
- * property is_paired:
- * """true if read is paired in sequencing"""
- * def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FPAIRED
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5query___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2431
+ * were not considered for alignment may have been retained."""
+ *
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
+ uint32_t __pyx_v_start;
+ uint32_t __pyx_v_end;
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2422);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(((((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2431);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
+ /* "csamtools.pyx":2436
+ * cdef char * s
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ *
+ * if src.core.l_qseq == 0: return None
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
+
+ /* "csamtools.pyx":2438
+ * src = self._delegate
+ *
+ * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ *
+ * start = query_start(src)
+ */
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2440
+ * if src.core.l_qseq == 0: return None
+ *
+ * start = query_start(src) # <<<<<<<<<<<<<<
+ * end = query_end(src)
+ *
+ */
+ __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_start = __pyx_t_2;
+
+ /* "csamtools.pyx":2441
+ *
+ * start = query_start(src)
+ * end = query_end(src) # <<<<<<<<<<<<<<
+ *
+ * return get_seq_range(src, start, end)
+ */
+ __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_end = __pyx_t_2;
+
+ /* "csamtools.pyx":2443
+ * end = query_end(src)
+ *
+ * return get_seq_range(src, start, end) # <<<<<<<<<<<<<<
+ *
+ * property qqual:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_3 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__get__");
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.AlignedRead.query.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2423
- * """true if read is paired in sequencing"""
- * def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FPAIRED
- * else: self._delegate.core.flag &= ~BAM_FPAIRED
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2449
+ *
+ * In Python 3, this property is of type bytes."""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * cdef uint32_t start, end
*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
+ uint32_t __pyx_v_start;
+ uint32_t __pyx_v_end;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
+ int32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2423);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2449);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2424
- * def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FPAIRED # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FPAIRED
- * property is_proper_pair:
+ /* "csamtools.pyx":2453
+ * cdef uint32_t start, end
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ *
+ * if src.core.l_qseq == 0: return None
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
+
+ /* "csamtools.pyx":2455
+ * src = self._delegate
+ *
+ * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
+ *
+ * start = query_start(src)
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 1;
- goto __pyx_L5;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
}
- /*else*/ {
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2425
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FPAIRED
- * else: self._delegate.core.flag &= ~BAM_FPAIRED # <<<<<<<<<<<<<<
- * property is_proper_pair:
- * """true if read is mapped in a proper pair"""
+ /* "csamtools.pyx":2457
+ * if src.core.l_qseq == 0: return None
+ *
+ * start = query_start(src) # <<<<<<<<<<<<<<
+ * end = query_end(src)
+ *
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~1);
- }
- __pyx_L5:;
+ __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_start = __pyx_t_2;
- __pyx_r = 0;
+ /* "csamtools.pyx":2458
+ *
+ * start = query_start(src)
+ * end = query_end(src) # <<<<<<<<<<<<<<
+ *
+ * return get_qual_range(src, start, end)
+ */
+ __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_end = __pyx_t_2;
+
+ /* "csamtools.pyx":2460
+ * end = query_end(src)
+ *
+ * return get_qual_range(src, start, end) # <<<<<<<<<<<<<<
+ *
+ * property qstart:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_3 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__set__");
- __pyx_r = -1;
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qqual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2428
- * property is_proper_pair:
- * """true if read is mapped in a proper pair"""
- * def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2464
+ * property qstart:
+ * """start index of the aligned query portion of the sequence (0-based, inclusive)"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return query_start(self._delegate)
+ *
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2428);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2464);
+
+ /* "csamtools.pyx":2465
+ * """start index of the aligned query portion of the sequence (0-based, inclusive)"""
+ * def __get__(self):
+ * return query_start(self._delegate) # <<<<<<<<<<<<<<
+ *
+ * property qend:
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_query_start(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.qstart.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2429
- * """true if read is mapped in a proper pair"""
- * def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
- * else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
- */
-
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2429);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2430
- * def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
- * property is_unmapped:
- */
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 2;
- goto __pyx_L5;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2431
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
- * else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
- * property is_unmapped:
- * """true if read itself is unmapped"""
- */
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~2);
- }
- __pyx_L5:;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qend___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2434
- * property is_unmapped:
- * """true if read itself is unmapped"""
- * def __get__(self): return (self.flag & BAM_FUNMAP) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FUNMAP
+/* "csamtools.pyx":2469
+ * property qend:
+ * """end index of the aligned query portion of the sequence (0-based, exclusive)"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return query_end(self._delegate)
+ *
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2434);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2469);
+
+ /* "csamtools.pyx":2470
+ * """end index of the aligned query portion of the sequence (0-based, exclusive)"""
+ * def __get__(self):
+ * return query_end(self._delegate) # <<<<<<<<<<<<<<
+ *
+ * property qlen:
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.qend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2435
- * """true if read itself is unmapped"""
- * def __get__(self): return (self.flag & BAM_FUNMAP) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FUNMAP
- * else: self._delegate.core.flag &= ~BAM_FUNMAP
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2474
+ * property qlen:
+ * """Length of the aligned query sequence"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * src = self._delegate
*/
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2435);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2436
- * def __get__(self): return (self.flag & BAM_FUNMAP) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FUNMAP # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FUNMAP
- * property mate_is_unmapped:
- */
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 4;
- goto __pyx_L5;
- }
- /*else*/ {
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2474);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2437
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FUNMAP
- * else: self._delegate.core.flag &= ~BAM_FUNMAP # <<<<<<<<<<<<<<
- * property mate_is_unmapped:
- * """true if the mate is unmapped"""
+ /* "csamtools.pyx":2476
+ * def __get__(self):
+ * cdef bam1_t * src
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * return query_end(src)-query_start(src)
+ *
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~4);
- }
- __pyx_L5:;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_v_src = __pyx_v_self->_delegate;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2440
- * property mate_is_unmapped:
- * """true if the mate is unmapped"""
- * def __get__(self): return (self.flag & BAM_FMUNMAP) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FMUNMAP
+ /* "csamtools.pyx":2477
+ * cdef bam1_t * src
+ * src = self._delegate
+ * return query_end(src)-query_start(src) # <<<<<<<<<<<<<<
+ *
+ * property tags:
*/
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2440);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong((__pyx_t_1 - __pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__get__");
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2441
- * """true if the mate is unmapped"""
- * def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FMUNMAP
- * else: self._delegate.core.flag &= ~BAM_FMUNMAP
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tags___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2494
+ * multiple times.
+ * """
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef char * ctag
+ * cdef bam1_t * src
*/
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
+ uint8_t *__pyx_v_s;
+ char __pyx_v_auxtag[3];
+ char __pyx_v_auxtype;
+ uint8_t __pyx_v_byte_size;
+ int32_t __pyx_v_nvalues;
+ PyObject *__pyx_v_result = NULL;
+ PyObject *__pyx_v_value = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ char __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ Py_ssize_t __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ uint8_t __pyx_t_12;
+ int32_t __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2441);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2494);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2442
- * def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FMUNMAP # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FMUNMAP
- * property is_reverse:
+ /* "csamtools.pyx":2503
+ * cdef int32_t nvalues
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.l_aux == 0: return []
+ * s = bam1_aux( src )
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 8;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2443
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FMUNMAP
- * else: self._delegate.core.flag &= ~BAM_FMUNMAP # <<<<<<<<<<<<<<
- * property is_reverse:
- * """true if read is mapped to reverse strand"""
+ /* "csamtools.pyx":2504
+ *
+ * src = self._delegate
+ * if src.l_aux == 0: return [] # <<<<<<<<<<<<<<
+ * s = bam1_aux( src )
+ * result = []
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~8);
+ __pyx_t_1 = (__pyx_v_src->l_aux == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
}
- __pyx_L5:;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_L3:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2446
- * property is_reverse:
- * """true if read is mapped to reverse strand"""
- * def __get__(self): return (self.flag & BAM_FREVERSE) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREVERSE
+ /* "csamtools.pyx":2505
+ * src = self._delegate
+ * if src.l_aux == 0: return []
+ * s = bam1_aux( src ) # <<<<<<<<<<<<<<
+ * result = []
+ * auxtag[2] = 0
*/
+ __pyx_v_s = bam1_aux(__pyx_v_src);
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2446);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /* "csamtools.pyx":2506
+ * if src.l_aux == 0: return []
+ * s = bam1_aux( src )
+ * result = [] # <<<<<<<<<<<<<<
+ * auxtag[2] = 0
+ * while s < (src.data + src.data_len):
+ */
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2447
- * """true if read is mapped to reverse strand"""
- * def __get__(self): return (self.flag & BAM_FREVERSE) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FREVERSE
- * else: self._delegate.core.flag &= ~BAM_FREVERSE
+ /* "csamtools.pyx":2507
+ * s = bam1_aux( src )
+ * result = []
+ * auxtag[2] = 0 # <<<<<<<<<<<<<<
+ * while s < (src.data + src.data_len):
+ * # get tag
*/
+ (__pyx_v_auxtag[2]) = 0;
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2447);
+ /* "csamtools.pyx":2508
+ * result = []
+ * auxtag[2] = 0
+ * while s < (src.data + src.data_len): # <<<<<<<<<<<<<<
+ * # get tag
+ * auxtag[0] = s[0]
+ */
+ while (1) {
+ __pyx_t_1 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
+ if (!__pyx_t_1) break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2448
- * def __get__(self): return (self.flag & BAM_FREVERSE) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREVERSE # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FREVERSE
- * property mate_is_reverse:
+ /* "csamtools.pyx":2510
+ * while s < (src.data + src.data_len):
+ * # get tag
+ * auxtag[0] = s[0] # <<<<<<<<<<<<<<
+ * auxtag[1] = s[1]
+ * s += 2
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 16;
- goto __pyx_L5;
- }
- /*else*/ {
+ (__pyx_v_auxtag[0]) = (__pyx_v_s[0]);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2449
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREVERSE
- * else: self._delegate.core.flag &= ~BAM_FREVERSE # <<<<<<<<<<<<<<
- * property mate_is_reverse:
- * """true is read is mapped to reverse strand"""
+ /* "csamtools.pyx":2511
+ * # get tag
+ * auxtag[0] = s[0]
+ * auxtag[1] = s[1] # <<<<<<<<<<<<<<
+ * s += 2
+ * auxtype = s[0]
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~16);
- }
- __pyx_L5:;
+ (__pyx_v_auxtag[1]) = (__pyx_v_s[1]);
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2512
+ * auxtag[0] = s[0]
+ * auxtag[1] = s[1]
+ * s += 2 # <<<<<<<<<<<<<<
+ * auxtype = s[0]
+ * if auxtype in ('c', 'C'):
+ */
+ __pyx_v_s = (__pyx_v_s + 2);
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2452
- * property mate_is_reverse:
- * """true is read is mapped to reverse strand"""
- * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FMREVERSE
+ /* "csamtools.pyx":2513
+ * auxtag[1] = s[1]
+ * s += 2
+ * auxtype = s[0] # <<<<<<<<<<<<<<
+ * if auxtype in ('c', 'C'):
+ * value = <int>bam_aux2i(s)
*/
+ __pyx_v_auxtype = (__pyx_v_s[0]);
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2452);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2514
+ * s += 2
+ * auxtype = s[0]
+ * if auxtype in ('c', 'C'): # <<<<<<<<<<<<<<
+ * value = <int>bam_aux2i(s)
+ * s += 1
+ */
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 'c'));
+ if (!__pyx_t_1) {
+ __pyx_t_4 = ((int)(__pyx_t_3 == 'C'));
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_1;
+ }
+ __pyx_t_1 = __pyx_t_5;
+ if (__pyx_t_1) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2453
- * """true is read is mapped to reverse strand"""
- * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FMREVERSE
- * else: self._delegate.core.flag &= ~BAM_FMREVERSE
+ /* "csamtools.pyx":2515
+ * auxtype = s[0]
+ * if auxtype in ('c', 'C'):
+ * value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
+ * s += 1
+ * elif auxtype in ('s', 'S'):
*/
+ __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2453);
+ /* "csamtools.pyx":2516
+ * if auxtype in ('c', 'C'):
+ * value = <int>bam_aux2i(s)
+ * s += 1 # <<<<<<<<<<<<<<
+ * elif auxtype in ('s', 'S'):
+ * value = <int>bam_aux2i(s)
+ */
+ __pyx_v_s = (__pyx_v_s + 1);
+ goto __pyx_L6;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2454
- * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FMREVERSE # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FMREVERSE
- * property is_read1:
+ /* "csamtools.pyx":2517
+ * value = <int>bam_aux2i(s)
+ * s += 1
+ * elif auxtype in ('s', 'S'): # <<<<<<<<<<<<<<
+ * value = <int>bam_aux2i(s)
+ * s += 2
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 32;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 's'));
+ if (!__pyx_t_1) {
+ __pyx_t_5 = ((int)(__pyx_t_3 == 'S'));
+ __pyx_t_4 = __pyx_t_5;
+ } else {
+ __pyx_t_4 = __pyx_t_1;
+ }
+ __pyx_t_1 = __pyx_t_4;
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2455
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FMREVERSE
- * else: self._delegate.core.flag &= ~BAM_FMREVERSE # <<<<<<<<<<<<<<
- * property is_read1:
- * """true if this is read1"""
+ /* "csamtools.pyx":2518
+ * s += 1
+ * elif auxtype in ('s', 'S'):
+ * value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
+ * s += 2
+ * elif auxtype in ('i', 'I'):
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~32);
- }
- __pyx_L5:;
+ __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2519
+ * elif auxtype in ('s', 'S'):
+ * value = <int>bam_aux2i(s)
+ * s += 2 # <<<<<<<<<<<<<<
+ * elif auxtype in ('i', 'I'):
+ * value = <int32_t>bam_aux2i(s)
+ */
+ __pyx_v_s = (__pyx_v_s + 2);
+ goto __pyx_L6;
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2458
- * property is_read1:
- * """true if this is read1"""
- * def __get__(self): return (self.flag & BAM_FREAD1) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREAD1
+ /* "csamtools.pyx":2520
+ * value = <int>bam_aux2i(s)
+ * s += 2
+ * elif auxtype in ('i', 'I'): # <<<<<<<<<<<<<<
+ * value = <int32_t>bam_aux2i(s)
+ * s += 4
*/
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 'i'));
+ if (!__pyx_t_1) {
+ __pyx_t_4 = ((int)(__pyx_t_3 == 'I'));
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_1;
+ }
+ __pyx_t_1 = __pyx_t_5;
+ if (__pyx_t_1) {
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2458);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_64); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ /* "csamtools.pyx":2521
+ * s += 2
+ * elif auxtype in ('i', 'I'):
+ * value = <int32_t>bam_aux2i(s) # <<<<<<<<<<<<<<
+ * s += 4
+ * elif auxtype == 'f':
+ */
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2522
+ * elif auxtype in ('i', 'I'):
+ * value = <int32_t>bam_aux2i(s)
+ * s += 4 # <<<<<<<<<<<<<<
+ * elif auxtype == 'f':
+ * value = <float>bam_aux2f(s)
+ */
+ __pyx_v_s = (__pyx_v_s + 4);
+ goto __pyx_L6;
+ }
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2459
- * """true if this is read1"""
- * def __get__(self): return (self.flag & BAM_FREAD1) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FREAD1
- * else: self._delegate.core.flag &= ~BAM_FREAD1
+ /* "csamtools.pyx":2523
+ * value = <int32_t>bam_aux2i(s)
+ * s += 4
+ * elif auxtype == 'f': # <<<<<<<<<<<<<<
+ * value = <float>bam_aux2f(s)
+ * s += 4
*/
+ __pyx_t_1 = (__pyx_v_auxtype == 'f');
+ if (__pyx_t_1) {
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2459);
+ /* "csamtools.pyx":2524
+ * s += 4
+ * elif auxtype == 'f':
+ * value = <float>bam_aux2f(s) # <<<<<<<<<<<<<<
+ * s += 4
+ * elif auxtype == 'd':
+ */
+ __pyx_t_2 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2460
- * def __get__(self): return (self.flag & BAM_FREAD1) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREAD1 # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FREAD1
- * property is_read2:
+ /* "csamtools.pyx":2525
+ * elif auxtype == 'f':
+ * value = <float>bam_aux2f(s)
+ * s += 4 # <<<<<<<<<<<<<<
+ * elif auxtype == 'd':
+ * value = <double>bam_aux2d(s)
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 64;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_v_s = (__pyx_v_s + 4);
+ goto __pyx_L6;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2461
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREAD1
- * else: self._delegate.core.flag &= ~BAM_FREAD1 # <<<<<<<<<<<<<<
- * property is_read2:
- * """true if this is read2"""
+ /* "csamtools.pyx":2526
+ * value = <float>bam_aux2f(s)
+ * s += 4
+ * elif auxtype == 'd': # <<<<<<<<<<<<<<
+ * value = <double>bam_aux2d(s)
+ * s += 8
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~64);
- }
- __pyx_L5:;
+ __pyx_t_1 = (__pyx_v_auxtype == 'd');
+ if (__pyx_t_1) {
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2527
+ * s += 4
+ * elif auxtype == 'd':
+ * value = <double>bam_aux2d(s) # <<<<<<<<<<<<<<
+ * s += 8
+ * elif auxtype == 'A':
+ */
+ __pyx_t_2 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2464
- * property is_read2:
- * """true if this is read2"""
- * def __get__(self): return (self.flag & BAM_FREAD2) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREAD2
+ /* "csamtools.pyx":2528
+ * elif auxtype == 'd':
+ * value = <double>bam_aux2d(s)
+ * s += 8 # <<<<<<<<<<<<<<
+ * elif auxtype == 'A':
+ * value = "%c" % <char>bam_aux2A(s)
*/
+ __pyx_v_s = (__pyx_v_s + 8);
+ goto __pyx_L6;
+ }
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2464);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_128); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ /* "csamtools.pyx":2529
+ * value = <double>bam_aux2d(s)
+ * s += 8
+ * elif auxtype == 'A': # <<<<<<<<<<<<<<
+ * value = "%c" % <char>bam_aux2A(s)
+ * s += 1
+ */
+ __pyx_t_1 = (__pyx_v_auxtype == 'A');
+ if (__pyx_t_1) {
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2530
+ * s += 8
+ * elif auxtype == 'A':
+ * value = "%c" % <char>bam_aux2A(s) # <<<<<<<<<<<<<<
+ * s += 1
+ * elif auxtype in ('Z', 'H'):
+ */
+ __pyx_t_2 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = ((PyObject *)__pyx_t_6);
+ __pyx_t_6 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2465
- * """true if this is read2"""
- * def __get__(self): return (self.flag & BAM_FREAD2) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FREAD2
- * else: self._delegate.core.flag &= ~BAM_FREAD2
+ /* "csamtools.pyx":2531
+ * elif auxtype == 'A':
+ * value = "%c" % <char>bam_aux2A(s)
+ * s += 1 # <<<<<<<<<<<<<<
+ * elif auxtype in ('Z', 'H'):
+ * value = _charptr_to_str(<char*>bam_aux2Z(s))
*/
+ __pyx_v_s = (__pyx_v_s + 1);
+ goto __pyx_L6;
+ }
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2465);
+ /* "csamtools.pyx":2532
+ * value = "%c" % <char>bam_aux2A(s)
+ * s += 1
+ * elif auxtype in ('Z', 'H'): # <<<<<<<<<<<<<<
+ * value = _charptr_to_str(<char*>bam_aux2Z(s))
+ * # +1 for NULL terminated string
+ */
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 'Z'));
+ if (!__pyx_t_1) {
+ __pyx_t_5 = ((int)(__pyx_t_3 == 'H'));
+ __pyx_t_4 = __pyx_t_5;
+ } else {
+ __pyx_t_4 = __pyx_t_1;
+ }
+ __pyx_t_1 = __pyx_t_4;
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2466
- * def __get__(self): return (self.flag & BAM_FREAD2) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREAD2 # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FREAD2
- * property is_secondary:
+ /* "csamtools.pyx":2533
+ * s += 1
+ * elif auxtype in ('Z', 'H'):
+ * value = _charptr_to_str(<char*>bam_aux2Z(s)) # <<<<<<<<<<<<<<
+ * # +1 for NULL terminated string
+ * s += len(value) + 1
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 128;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_s))); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2467
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FREAD2
- * else: self._delegate.core.flag &= ~BAM_FREAD2 # <<<<<<<<<<<<<<
- * property is_secondary:
- * """true if not primary alignment"""
+ /* "csamtools.pyx":2535
+ * value = _charptr_to_str(<char*>bam_aux2Z(s))
+ * # +1 for NULL terminated string
+ * s += len(value) + 1 # <<<<<<<<<<<<<<
+ * elif auxtype == 'B':
+ * s += 1
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~128);
- }
- __pyx_L5:;
+ __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = (__pyx_v_s + (__pyx_t_7 + 1));
+ goto __pyx_L6;
+ }
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2536
+ * # +1 for NULL terminated string
+ * s += len(value) + 1
+ * elif auxtype == 'B': # <<<<<<<<<<<<<<
+ * s += 1
+ * byte_size, nvalues, value = convertBinaryTagToList( s )
+ */
+ __pyx_t_1 = (__pyx_v_auxtype == 'B');
+ if (__pyx_t_1) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2470
- * property is_secondary:
- * """true if not primary alignment"""
- * def __get__(self): return (self.flag & BAM_FSECONDARY) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FSECONDARY
+ /* "csamtools.pyx":2537
+ * s += len(value) + 1
+ * elif auxtype == 'B':
+ * s += 1 # <<<<<<<<<<<<<<
+ * byte_size, nvalues, value = convertBinaryTagToList( s )
+ * # 5 for 1 char and 1 int
*/
+ __pyx_v_s = (__pyx_v_s + 1);
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2470);
+ /* "csamtools.pyx":2538
+ * elif auxtype == 'B':
+ * s += 1
+ * byte_size, nvalues, value = convertBinaryTagToList( s ) # <<<<<<<<<<<<<<
+ * # 5 for 1 char and 1 int
+ * s += 5 + ( nvalues * byte_size) - 1
+ */
+ __pyx_t_6 = __pyx_f_9csamtools_convertBinaryTagToList(__pyx_v_s); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
+ PyObject* sequence = __pyx_t_6;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
+ if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 2);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
+ if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 2);
+ }
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_8);
+ index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L8_unpacking_done:;
+ }
+ __pyx_t_12 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_2); if (unlikely((__pyx_t_12 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_13 = __Pyx_PyInt_from_py_int32_t(__pyx_t_8); if (unlikely((__pyx_t_13 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_byte_size = __pyx_t_12;
+ __pyx_v_nvalues = __pyx_t_13;
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_9;
+ __pyx_t_9 = 0;
+
+ /* "csamtools.pyx":2540
+ * byte_size, nvalues, value = convertBinaryTagToList( s )
+ * # 5 for 1 char and 1 int
+ * s += 5 + ( nvalues * byte_size) - 1 # <<<<<<<<<<<<<<
+ *
+ * s += 1
+ */
+ __pyx_v_s = (__pyx_v_s + ((5 + (__pyx_v_nvalues * __pyx_v_byte_size)) - 1));
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+
+ /* "csamtools.pyx":2542
+ * s += 5 + ( nvalues * byte_size) - 1
+ *
+ * s += 1 # <<<<<<<<<<<<<<
+ *
+ * result.append( (_charptr_to_str(auxtag), value) )
+ */
+ __pyx_v_s = (__pyx_v_s + 1);
+
+ /* "csamtools.pyx":2544
+ * s += 1
+ *
+ * result.append( (_charptr_to_str(auxtag), value) ) # <<<<<<<<<<<<<<
+ *
+ * return result
+ */
+ __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_value);
+ __Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_6 = 0;
+ __pyx_t_14 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ }
+
+ /* "csamtools.pyx":2546
+ * result.append( (_charptr_to_str(auxtag), value) )
+ *
+ * return result # <<<<<<<<<<<<<<
+ *
+ * def __set__(self, tags):
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_256); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_v_result));
+ __pyx_r = ((PyObject *)__pyx_v_result);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__get__");
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tags.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_result);
+ __Pyx_XDECREF(__pyx_v_value);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2471
- * """true if not primary alignment"""
- * def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FSECONDARY
- * else: self._delegate.core.flag &= ~BAM_FSECONDARY
- */
-
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2471);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2472
- * def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FSECONDARY # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FSECONDARY
- * property is_qcfail:
- */
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 256;
- goto __pyx_L5;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2473
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FSECONDARY
- * else: self._delegate.core.flag &= ~BAM_FSECONDARY # <<<<<<<<<<<<<<
- * property is_qcfail:
- * """true if QC failure"""
- */
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~256);
- }
- __pyx_L5:;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tags));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2476
- * property is_qcfail:
- * """true if QC failure"""
- * def __get__(self): return (self.flag & BAM_FQCFAIL) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FQCFAIL
+/* "csamtools.pyx":2548
+ * return result
+ *
+ * def __set__(self, tags): # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * cdef uint8_t * s
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags) {
+ bam1_t *__pyx_v_src;
+ uint8_t *__pyx_v_s;
+ char *__pyx_v_temp;
+ PyObject *__pyx_v_fmts = NULL;
+ PyObject *__pyx_v_args = NULL;
+ PyObject *__pyx_v_pytag = NULL;
+ PyObject *__pyx_v_value = NULL;
+ PyObject *__pyx_v_t = NULL;
+ PyObject *__pyx_v_pytype = NULL;
+ PyObject *__pyx_v_datafmt = NULL;
+ PyObject *__pyx_v_datatype = NULL;
+ PyObject *__pyx_v_mi = NULL;
+ PyObject *__pyx_v_ma = NULL;
+ PyObject *__pyx_v_absmax = NULL;
+ PyObject *__pyx_v_fmt = NULL;
+ PyObject *__pyx_v_total_size = NULL;
+ PyObject *__pyx_v_buffer = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ Py_ssize_t __pyx_t_4;
+ PyObject *(*__pyx_t_5)(PyObject *);
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ Py_ssize_t __pyx_t_12;
+ PyObject *__pyx_t_13 = NULL;
+ PyObject *__pyx_t_14 = NULL;
+ int __pyx_t_15;
+ size_t __pyx_t_16;
+ int __pyx_t_17;
+ char *__pyx_t_18;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2476);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2548);
+
+ /* "csamtools.pyx":2554
+ * cdef char * temp
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ *
+ * fmts, args = ["<"], []
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
+
+ /* "csamtools.pyx":2556
+ * src = self._delegate
+ *
+ * fmts, args = ["<"], [] # <<<<<<<<<<<<<<
+ *
+ * if tags != None:
+ */
+ __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_512); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_138));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_138));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138));
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
+ __pyx_v_fmts = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_v_args = __pyx_t_2;
+ __pyx_t_2 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2477
- * """true if QC failure"""
- * def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FQCFAIL
- * else: self._delegate.core.flag &= ~BAM_FQCFAIL
+ /* "csamtools.pyx":2558
+ * fmts, args = ["<"], []
+ *
+ * if tags != None: # <<<<<<<<<<<<<<
+ *
+ * # map samtools code to python.struct code and byte size
*/
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_tags, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_3) {
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2477);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2478
- * def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FQCFAIL # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FQCFAIL
- * property is_duplicate:
+ /* "csamtools.pyx":2561
+ *
+ * # map samtools code to python.struct code and byte size
+ * for pytag, value in tags: # <<<<<<<<<<<<<<
+ * if not type(pytag) is bytes:
+ * pytag = pytag.encode('ascii')
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 512;
- goto __pyx_L5;
- }
- /*else*/ {
+ if (PyList_CheckExact(__pyx_v_tags) || PyTuple_CheckExact(__pyx_v_tags)) {
+ __pyx_t_2 = __pyx_v_tags; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_5 = NULL;
+ } else {
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_tags); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_5 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ }
+ for (;;) {
+ if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
+ } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
+ } else {
+ __pyx_t_1 = __pyx_t_5(__pyx_t_2);
+ if (unlikely(!__pyx_t_1)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_1);
+ }
+ if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
+ PyObject* sequence = __pyx_t_1;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
+ }
+ __Pyx_XDECREF(__pyx_v_pytag);
+ __pyx_v_pytag = __pyx_t_6;
+ __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2479
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FQCFAIL
- * else: self._delegate.core.flag &= ~BAM_FQCFAIL # <<<<<<<<<<<<<<
- * property is_duplicate:
- * """true if optical or PCR duplicate"""
+ /* "csamtools.pyx":2562
+ * # map samtools code to python.struct code and byte size
+ * for pytag, value in tags:
+ * if not type(pytag) is bytes: # <<<<<<<<<<<<<<
+ * pytag = pytag.encode('ascii')
+ * t = type(value)
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~512);
- }
- __pyx_L5:;
+ __pyx_t_3 = (((PyObject *)Py_TYPE(__pyx_v_pytag)) == ((PyObject *)((PyObject*)(&PyBytes_Type))));
+ __pyx_t_10 = (!__pyx_t_3);
+ if (__pyx_t_10) {
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2563
+ * for pytag, value in tags:
+ * if not type(pytag) is bytes:
+ * pytag = pytag.encode('ascii') # <<<<<<<<<<<<<<
+ * t = type(value)
+ *
+ */
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_pytag, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_v_pytag);
+ __pyx_v_pytag = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2482
- * property is_duplicate:
- * """true if optical or PCR duplicate"""
- * def __get__(self): return (self.flag & BAM_FDUP) != 0 # <<<<<<<<<<<<<<
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FDUP
+ /* "csamtools.pyx":2564
+ * if not type(pytag) is bytes:
+ * pytag = pytag.encode('ascii')
+ * t = type(value) # <<<<<<<<<<<<<<
+ *
+ * if t is tuple or t is list:
*/
+ __Pyx_INCREF(((PyObject *)Py_TYPE(__pyx_v_value)));
+ __Pyx_XDECREF(((PyObject *)__pyx_v_t));
+ __pyx_v_t = ((PyObject*)((PyObject *)Py_TYPE(__pyx_v_value)));
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2482);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_1024); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ /* "csamtools.pyx":2566
+ * t = type(value)
+ *
+ * if t is tuple or t is list: # <<<<<<<<<<<<<<
+ * # binary tags - treat separately
+ * pytype = 'B'
+ */
+ __pyx_t_10 = (__pyx_v_t == ((PyObject*)(&PyTuple_Type)));
+ if (!__pyx_t_10) {
+ __pyx_t_3 = (__pyx_v_t == ((PyObject*)(&PyList_Type)));
+ __pyx_t_11 = __pyx_t_3;
+ } else {
+ __pyx_t_11 = __pyx_t_10;
+ }
+ if (__pyx_t_11) {
+
+ /* "csamtools.pyx":2568
+ * if t is tuple or t is list:
+ * # binary tags - treat separately
+ * pytype = 'B' # <<<<<<<<<<<<<<
+ * # get data type - first value determines type
+ * if type(value[0]) is float:
+ */
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__B));
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = ((PyObject *)__pyx_n_s__B);
+
+ /* "csamtools.pyx":2570
+ * pytype = 'B'
+ * # get data type - first value determines type
+ * if type(value[0]) is float: # <<<<<<<<<<<<<<
+ * datafmt, datatype = "f", "f"
+ * else:
+ */
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_value, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = (((PyObject *)Py_TYPE(__pyx_t_7)) == ((PyObject *)((PyObject*)(&PyFloat_Type))));
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2571
+ * # get data type - first value determines type
+ * if type(value[0]) is float:
+ * datafmt, datatype = "f", "f" # <<<<<<<<<<<<<<
+ * else:
+ * mi, ma = min(value), max(value)
+ */
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L10;
+ }
+ /*else*/ {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2483
- * """true if optical or PCR duplicate"""
- * def __get__(self): return (self.flag & BAM_FDUP) != 0
- * def __set__(self,val): # <<<<<<<<<<<<<<
- * if val: self._delegate.core.flag |= BAM_FDUP
- * else: self._delegate.core.flag &= ~BAM_FDUP
+ /* "csamtools.pyx":2573
+ * datafmt, datatype = "f", "f"
+ * else:
+ * mi, ma = min(value), max(value) # <<<<<<<<<<<<<<
+ * absmax = max( abs(mi), abs(ma) )
+ * # signed ints
*/
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
+ __Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
+ __Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_max, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_v_mi);
+ __pyx_v_mi = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_ma);
+ __pyx_v_ma = __pyx_t_6;
+ __pyx_t_6 = 0;
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- int __pyx_t_1;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2483);
+ /* "csamtools.pyx":2574
+ * else:
+ * mi, ma = min(value), max(value)
+ * absmax = max( abs(mi), abs(ma) ) # <<<<<<<<<<<<<<
+ * # signed ints
+ * if mi < 0:
+ */
+ __pyx_t_6 = PyNumber_Absolute(__pyx_v_ma); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyNumber_Absolute(__pyx_v_mi); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_6, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_11) {
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = __pyx_t_6;
+ } else {
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_1 = __pyx_t_7;
+ }
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_v_absmax);
+ __pyx_v_absmax = __pyx_t_1;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2484
- * def __get__(self): return (self.flag & BAM_FDUP) != 0
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FDUP # <<<<<<<<<<<<<<
- * else: self._delegate.core.flag &= ~BAM_FDUP
- * property positions:
+ /* "csamtools.pyx":2576
+ * absmax = max( abs(mi), abs(ma) )
+ * # signed ints
+ * if mi < 0: # <<<<<<<<<<<<<<
+ * if mi >= -127: datafmt, datatype = "b", 'c'
+ * elif mi >= -32767: datafmt, datatype = "h", 's'
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag |= 1024;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+
+ /* "csamtools.pyx":2577
+ * # signed ints
+ * if mi < 0:
+ * if mi >= -127: datafmt, datatype = "b", 'c' # <<<<<<<<<<<<<<
+ * elif mi >= -32767: datafmt, datatype = "h", 's'
+ * elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ */
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__b);
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__c);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_6;
+ __pyx_t_6 = 0;
+ goto __pyx_L12;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2485
- * def __set__(self,val):
- * if val: self._delegate.core.flag |= BAM_FDUP
- * else: self._delegate.core.flag &= ~BAM_FDUP # <<<<<<<<<<<<<<
- * property positions:
- * """a list of reference positions that this read aligns to."""
+ /* "csamtools.pyx":2578
+ * if mi < 0:
+ * if mi >= -127: datafmt, datatype = "b", 'c'
+ * elif mi >= -32767: datafmt, datatype = "h", 's' # <<<<<<<<<<<<<<
+ * elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: datafmt, datatype = "i", 'i'
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag &= (~1024);
- }
- __pyx_L5:;
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__h);
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__s);
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_6;
+ __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L12;
+ }
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__set__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ /* "csamtools.pyx":2579
+ * if mi >= -127: datafmt, datatype = "b", 'c'
+ * elif mi >= -32767: datafmt, datatype = "h", 's'
+ * elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
+ * else: datafmt, datatype = "i", 'i'
+ *
+ */
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L12;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2580
+ * elif mi >= -32767: datafmt, datatype = "h", 's'
+ * elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: datafmt, datatype = "i", 'i' # <<<<<<<<<<<<<<
+ *
+ * # unsigned ints
+ */
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_6;
+ __pyx_t_6 = 0;
+ }
+ __pyx_L12:;
+ goto __pyx_L11;
+ }
+ /*else*/ {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2488
- * property positions:
- * """a list of reference positions that this read aligns to."""
- * def __get__(self): # <<<<<<<<<<<<<<
- * cdef uint32_t k, i, pos
- * cdef int op
+ /* "csamtools.pyx":2584
+ * # unsigned ints
+ * else:
+ * if absmax <= 255: datafmt, datatype = "B", 'C' # <<<<<<<<<<<<<<
+ * elif absmax <= 65535: datafmt, datatype = "H", 'S'
+ * elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__B);
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__C);
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_6;
+ __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L13;
+ }
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self) {
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_i;
- uint32_t __pyx_v_pos;
- int __pyx_v_op;
- uint32_t *__pyx_v_cigar_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_result;
- PyObject *__pyx_v_l;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- uint32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
- uint32_t __pyx_t_5;
- int __pyx_t_6;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2488);
- __pyx_v_result = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_l = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2585
+ * else:
+ * if absmax <= 255: datafmt, datatype = "B", 'C'
+ * elif absmax <= 65535: datafmt, datatype = "H", 'S' # <<<<<<<<<<<<<<
+ * elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: datafmt, datatype = "I", 'I'
+ */
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__H);
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__S);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_6;
+ __pyx_t_6 = 0;
+ goto __pyx_L13;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2494
- * cdef bam1_t * src
+ /* "csamtools.pyx":2586
+ * if absmax <= 255: datafmt, datatype = "B", 'C'
+ * elif absmax <= 65535: datafmt, datatype = "H", 'S'
+ * elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
+ * else: datafmt, datatype = "I", 'I'
*
- * result = [] # <<<<<<<<<<<<<<
- * src = self._delegate
- * if src.core.n_cigar == 0: return []
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_result));
- __pyx_v_result = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_Raise(__pyx_t_6, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L13;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2587
+ * elif absmax <= 65535: datafmt, datatype = "H", 'S'
+ * elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: datafmt, datatype = "I", 'I' # <<<<<<<<<<<<<<
+ *
+ * datafmt = "2sccI%i%s" % (len(value), datafmt)
+ */
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = __pyx_t_6;
+ __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ }
+ __pyx_L13:;
+ }
+ __pyx_L11:;
+ }
+ __pyx_L10:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2495
- *
- * result = []
- * src = self._delegate # <<<<<<<<<<<<<<
- * if src.core.n_cigar == 0: return []
+ /* "csamtools.pyx":2589
+ * else: datafmt, datatype = "I", 'I'
*
+ * datafmt = "2sccI%i%s" % (len(value), datafmt) # <<<<<<<<<<<<<<
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'),
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_datafmt);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_datafmt);
+ __Pyx_GIVEREF(__pyx_v_datafmt);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_141), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_v_datafmt);
+ __pyx_v_datafmt = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2496
- * result = []
- * src = self._delegate
- * if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2590
*
- * pos = src.core.pos
+ * datafmt = "2sccI%i%s" % (len(value), datafmt)
+ * args.extend( [pytag[:2], # <<<<<<<<<<<<<<
+ * pytype.encode('ascii'),
+ * datatype.encode('ascii'),
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_2) {
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2498
- * if src.core.n_cigar == 0: return []
+ /* "csamtools.pyx":2593
+ * pytype.encode('ascii'),
+ * datatype.encode('ascii'),
+ * len(value)] + list(value) ) # <<<<<<<<<<<<<<
+ * fmts.append( datafmt )
+ * continue
+ */
+ __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+
+ /* "csamtools.pyx":2591
+ * datafmt = "2sccI%i%s" % (len(value), datafmt)
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'), # <<<<<<<<<<<<<<
+ * datatype.encode('ascii'),
+ * len(value)] + list(value) )
+ */
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_142), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+
+ /* "csamtools.pyx":2592
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'),
+ * datatype.encode('ascii'), # <<<<<<<<<<<<<<
+ * len(value)] + list(value) )
+ * fmts.append( datafmt )
+ */
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_datatype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_13 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_143), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+
+ /* "csamtools.pyx":2593
+ * pytype.encode('ascii'),
+ * datatype.encode('ascii'),
+ * len(value)] + list(value) ) # <<<<<<<<<<<<<<
+ * fmts.append( datafmt )
+ * continue
+ */
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_14 = PyList_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ PyList_SET_ITEM(__pyx_t_14, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ PyList_SET_ITEM(__pyx_t_14, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ PyList_SET_ITEM(__pyx_t_14, 2, __pyx_t_13);
+ __Pyx_GIVEREF(__pyx_t_13);
+ PyList_SET_ITEM(__pyx_t_14, 3, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_6 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_13 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(__pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
+ __Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Add(((PyObject *)__pyx_t_14), __pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+
+ /* "csamtools.pyx":2594
+ * datatype.encode('ascii'),
+ * len(value)] + list(value) )
+ * fmts.append( datafmt ) # <<<<<<<<<<<<<<
+ * continue
*
- * pos = src.core.pos # <<<<<<<<<<<<<<
+ */
+ __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":2595
+ * len(value)] + list(value) )
+ * fmts.append( datafmt )
+ * continue # <<<<<<<<<<<<<<
*
- * cigar_p = bam1_cigar(src)
+ * if t is float:
*/
- __pyx_v_pos = __pyx_v_src->core.pos;
+ goto __pyx_L4_continue;
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2500
- * pos = src.core.pos
+ /* "csamtools.pyx":2597
+ * continue
*
- * cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
+ * if t is float: # <<<<<<<<<<<<<<
+ * fmt, pytype = "2scf", 'f'
+ * elif t is int:
*/
- __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
+ __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyFloat_Type)));
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2501
+ /* "csamtools.pyx":2598
*
- * cigar_p = bam1_cigar(src)
- * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * if t is float:
+ * fmt, pytype = "2scf", 'f' # <<<<<<<<<<<<<<
+ * elif t is int:
+ * # negative values
*/
- __pyx_t_3 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scf);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L14;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2502
- * cigar_p = bam1_cigar(src)
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- * if op == BAM_CMATCH:
+ /* "csamtools.pyx":2599
+ * if t is float:
+ * fmt, pytype = "2scf", 'f'
+ * elif t is int: # <<<<<<<<<<<<<<
+ * # negative values
+ * if value < 0:
*/
- __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
+ __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyInt_Type)));
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2503
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
- * if op == BAM_CMATCH:
- * for i from pos <= i < pos + l:
+ /* "csamtools.pyx":2601
+ * elif t is int:
+ * # negative values
+ * if value < 0: # <<<<<<<<<<<<<<
+ * if value >= -127: fmt, pytype = "2scb", 'c'
+ * elif value >= -32767: fmt, pytype = "2sch", 's'
*/
- __pyx_t_1 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2504
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- * if op == BAM_CMATCH: # <<<<<<<<<<<<<<
- * for i from pos <= i < pos + l:
- * result.append( i )
+ /* "csamtools.pyx":2602
+ * # negative values
+ * if value < 0:
+ * if value >= -127: fmt, pytype = "2scb", 'c' # <<<<<<<<<<<<<<
+ * elif value >= -32767: fmt, pytype = "2sch", 's'
+ * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_2 = (__pyx_v_op == 0);
- if (__pyx_t_2) {
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_13 = ((PyObject *)__pyx_kp_s__2scb);
+ __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__c);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_13;
+ __pyx_t_13 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L16;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2505
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- * if op == BAM_CMATCH:
- * for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
- * result.append( i )
- *
+ /* "csamtools.pyx":2603
+ * if value < 0:
+ * if value >= -127: fmt, pytype = "2scb", 'c'
+ * elif value >= -32767: fmt, pytype = "2sch", 's' # <<<<<<<<<<<<<<
+ * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: fmt, pytype = "2sci", 'i'
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyNumber_Add(__pyx_t_1, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2sch);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__s);
+ __Pyx_INCREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L16;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2506
- * if op == BAM_CMATCH:
- * for i from pos <= i < pos + l:
- * result.append( i ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2604
+ * if value >= -127: fmt, pytype = "2scb", 'c'
+ * elif value >= -32767: fmt, pytype = "2sch", 's'
+ * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
+ * else: fmt, pytype = "2sci", 'i'
+ * # positive values
+ */
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_13));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_13));
+ __pyx_t_13 = 0;
+ __pyx_t_13 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_13, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L16;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2605
+ * elif value >= -32767: fmt, pytype = "2sch", 's'
+ * elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: fmt, pytype = "2sci", 'i' # <<<<<<<<<<<<<<
+ * # positive values
+ * else:
+ */
+ __pyx_t_13 = ((PyObject *)__pyx_kp_s__2sci);
+ __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_13;
+ __pyx_t_13 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ }
+ __pyx_L16:;
+ goto __pyx_L15;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2608
+ * # positive values
+ * else:
+ * if value <= 255: fmt, pytype = "2scB", 'C' # <<<<<<<<<<<<<<
+ * elif value <= 65535: fmt, pytype = "2scH", 'S'
+ * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ */
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scB);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__C);
+ __Pyx_INCREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L17;
+ }
+
+ /* "csamtools.pyx":2609
+ * else:
+ * if value <= 255: fmt, pytype = "2scB", 'C'
+ * elif value <= 65535: fmt, pytype = "2scH", 'S' # <<<<<<<<<<<<<<
+ * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: fmt, pytype = "2scI", 'I'
+ */
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_13 = ((PyObject *)__pyx_kp_s__2scH);
+ __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__S);
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_13;
+ __pyx_t_13 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L17;
+ }
+
+ /* "csamtools.pyx":2610
+ * if value <= 255: fmt, pytype = "2scB", 'C'
+ * elif value <= 65535: fmt, pytype = "2scH", 'S'
+ * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
+ * else: fmt, pytype = "2scI", 'I'
+ * else:
+ */
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L17;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2611
+ * elif value <= 65535: fmt, pytype = "2scH", 'S'
+ * elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
+ * else: fmt, pytype = "2scI", 'I' # <<<<<<<<<<<<<<
+ * else:
+ * # Note: hex strings (H) are not supported yet
+ */
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scI);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ }
+ __pyx_L17:;
+ }
+ __pyx_L15:;
+ goto __pyx_L14;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2614
+ * else:
+ * # Note: hex strings (H) are not supported yet
+ * if t is not bytes: # <<<<<<<<<<<<<<
+ * value = value.encode('ascii')
+ * if len(value) == 1:
+ */
+ __pyx_t_11 = (__pyx_v_t != ((PyObject*)(&PyBytes_Type)));
+ if (__pyx_t_11) {
+
+ /* "csamtools.pyx":2615
+ * # Note: hex strings (H) are not supported yet
+ * if t is not bytes:
+ * value = value.encode('ascii') # <<<<<<<<<<<<<<
+ * if len(value) == 1:
+ * fmt, pytype = "2scc", 'A'
+ */
+ __pyx_t_13 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__encode); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_7 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_k_tuple_144), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L18;
+ }
+ __pyx_L18:;
+
+ /* "csamtools.pyx":2616
+ * if t is not bytes:
+ * value = value.encode('ascii')
+ * if len(value) == 1: # <<<<<<<<<<<<<<
+ * fmt, pytype = "2scc", 'A'
+ * else:
+ */
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = (__pyx_t_12 == 1);
+ if (__pyx_t_11) {
+
+ /* "csamtools.pyx":2617
+ * value = value.encode('ascii')
+ * if len(value) == 1:
+ * fmt, pytype = "2scc", 'A' # <<<<<<<<<<<<<<
+ * else:
+ * fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
+ */
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scc);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__A);
+ __Pyx_INCREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L19;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2619
+ * fmt, pytype = "2scc", 'A'
+ * else:
+ * fmt, pytype = "2sc%is" % (len(value)+1), 'Z' # <<<<<<<<<<<<<<
*
- * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ * args.extend( [pytag[:2],
*/
- if (unlikely(__pyx_v_result == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyInt_FromSsize_t((__pyx_t_12 + 1)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_145), __pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__Z);
+ __Pyx_INCREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = ((PyObject *)__pyx_t_7);
+ __pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
}
- __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyList_Append(((PyObject *)__pyx_v_result), __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_L19:;
}
- goto __pyx_L8;
- }
- __pyx_L8:;
+ __pyx_L14:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2508
- * result.append( i )
+ /* "csamtools.pyx":2621
+ * fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
*
- * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
- * pos += l
+ * args.extend( [pytag[:2], # <<<<<<<<<<<<<<
+ * pytype.encode('ascii'),
+ * value ] )
+ */
+ __pyx_t_13 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+
+ /* "csamtools.pyx":2622
+ *
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'), # <<<<<<<<<<<<<<
+ * value ] )
*
*/
- switch (__pyx_v_op) {
- case 0:
- case 2:
- case 3:
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_146), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2509
+ /* "csamtools.pyx":2623
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'),
+ * value ] ) # <<<<<<<<<<<<<<
*
- * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
- * pos += l # <<<<<<<<<<<<<<
+ * fmts.append( fmt )
+ */
+ __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ __Pyx_INCREF(__pyx_v_value);
+ PyList_SET_ITEM(__pyx_t_1, 2, __pyx_v_value);
+ __Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_7 = 0;
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2625
+ * value ] )
*
- * return result
+ * fmts.append( fmt ) # <<<<<<<<<<<<<<
+ *
+ * fmt = "".join(fmts)
*/
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_l); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_pos += __pyx_t_5;
- break;
+ __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L4_continue:;
}
- }
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2511
- * pos += l
+ /* "csamtools.pyx":2627
+ * fmts.append( fmt )
*
- * return result # <<<<<<<<<<<<<<
- * def overlap( self, uint32_t start, uint32_t end ):
- * """return number of bases on reference overlapping *start* and *end*
+ * fmt = "".join(fmts) # <<<<<<<<<<<<<<
+ * total_size = struct.calcsize(fmt)
+ * buffer = ctypes.create_string_buffer(total_size)
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_result));
- __pyx_r = ((PyObject *)__pyx_v_result);
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.AlignedRead.positions.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_result);
- __Pyx_DECREF(__pyx_v_l);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)__pyx_v_fmts));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fmts));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_fmts));
+ __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __pyx_v_fmt = __pyx_t_14;
+ __pyx_t_14 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2512
+ /* "csamtools.pyx":2628
*
- * return result
- * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
- * """return number of bases on reference overlapping *start* and *end*
- * """
+ * fmt = "".join(fmts)
+ * total_size = struct.calcsize(fmt) # <<<<<<<<<<<<<<
+ * buffer = ctypes.create_string_buffer(total_size)
+ * struct.pack_into( fmt,
*/
+ __pyx_t_14 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_14, __pyx_n_s__calcsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_INCREF(__pyx_v_fmt);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_fmt);
+ __Pyx_GIVEREF(__pyx_v_fmt);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __pyx_v_total_size = __pyx_t_2;
+ __pyx_t_2 = 0;
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of bases on reference overlapping *start* and *end*\n ";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- uint32_t __pyx_v_start;
- uint32_t __pyx_v_end;
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_pos;
- uint32_t __pyx_v_overlap;
- int __pyx_v_op;
- int __pyx_v_o;
- uint32_t *__pyx_v_cigar_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_l;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- uint32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- uint32_t __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- uint32_t __pyx_t_8;
- uint32_t __pyx_t_9;
- int __pyx_t_10;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("overlap");
- __Pyx_TraceCall("overlap", __pyx_f[0], 2512);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(values[0]); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(values[1]); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.overlap");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_l = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2520
- * cdef bam1_t * src
- *
- * overlap = 0 # <<<<<<<<<<<<<<
- *
- * src = self._delegate
+ /* "csamtools.pyx":2629
+ * fmt = "".join(fmts)
+ * total_size = struct.calcsize(fmt)
+ * buffer = ctypes.create_string_buffer(total_size) # <<<<<<<<<<<<<<
+ * struct.pack_into( fmt,
+ * buffer,
*/
- __pyx_v_overlap = 0;
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__ctypes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_14 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s_147); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_total_size);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_total_size);
+ __Pyx_GIVEREF(__pyx_v_total_size);
+ __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_v_buffer = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2522
- * overlap = 0
- *
- * src = self._delegate # <<<<<<<<<<<<<<
- * if src.core.n_cigar == 0: return 0
- * pos = src.core.pos
+ /* "csamtools.pyx":2630
+ * total_size = struct.calcsize(fmt)
+ * buffer = ctypes.create_string_buffer(total_size)
+ * struct.pack_into( fmt, # <<<<<<<<<<<<<<
+ * buffer,
+ * 0,
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__pack_into); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2523
- *
- * src = self._delegate
- * if src.core.n_cigar == 0: return 0 # <<<<<<<<<<<<<<
- * pos = src.core.pos
- * o = 0
+ /* "csamtools.pyx":2631
+ * buffer = ctypes.create_string_buffer(total_size)
+ * struct.pack_into( fmt,
+ * buffer, # <<<<<<<<<<<<<<
+ * 0,
+ * *args )
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_1) {
- __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_fmt);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fmt);
+ __Pyx_GIVEREF(__pyx_v_fmt);
+ __Pyx_INCREF(__pyx_v_buffer);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_buffer);
+ __Pyx_GIVEREF(__pyx_v_buffer);
__Pyx_INCREF(__pyx_int_0);
- __pyx_r = __pyx_int_0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
- __pyx_L6:;
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2524
- * src = self._delegate
- * if src.core.n_cigar == 0: return 0
- * pos = src.core.pos # <<<<<<<<<<<<<<
- * o = 0
+ /* "csamtools.pyx":2633
+ * buffer,
+ * 0,
+ * *args ) # <<<<<<<<<<<<<<
*
+ * # delete the old data and allocate new space.
*/
- __pyx_v_pos = __pyx_v_src->core.pos;
+ __pyx_t_14 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ __pyx_t_13 = PyNumber_Add(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2525
- * if src.core.n_cigar == 0: return 0
- * pos = src.core.pos
- * o = 0 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2640
+ * pysam_bam_update( src,
+ * src.l_aux,
+ * total_size, # <<<<<<<<<<<<<<
+ * bam1_aux( src ) )
*
- * cigar_p = bam1_cigar(src)
*/
- __pyx_v_o = 0;
+ if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2527
- * o = 0
+ /* "csamtools.pyx":2641
+ * src.l_aux,
+ * total_size,
+ * bam1_aux( src ) ) # <<<<<<<<<<<<<<
*
- * cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
+ * src.l_aux = total_size
*/
- __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
+ pysam_bam_update(__pyx_v_src, __pyx_v_src->l_aux, __pyx_t_16, bam1_aux(__pyx_v_src));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2528
+ /* "csamtools.pyx":2643
+ * bam1_aux( src ) )
*
- * cigar_p = bam1_cigar(src)
- * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
- */
- __pyx_t_2 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_2; __pyx_v_k++) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2529
- * cigar_p = bam1_cigar(src)
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * src.l_aux = total_size # <<<<<<<<<<<<<<
*
+ * # copy data only if there is any
*/
- __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
+ __pyx_t_17 = __Pyx_PyInt_AsInt(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_src->l_aux = __pyx_t_17;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2530
- * for k from 0 <= k < src.core.n_cigar:
- * op = cigar_p[k] & BAM_CIGAR_MASK
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2646
*
- * if op == BAM_CMATCH:
- */
- __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_3;
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2532
- * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * # copy data only if there is any
+ * if total_size != 0: # <<<<<<<<<<<<<<
*
- * if op == BAM_CMATCH: # <<<<<<<<<<<<<<
- * o = min( pos + l, end) - max( pos, start )
- * if o > 0: overlap += o
+ * # get location of new data
*/
- __pyx_t_1 = (__pyx_v_op == 0);
- if (__pyx_t_1) {
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_total_size, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ if (__pyx_t_11) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2533
+ /* "csamtools.pyx":2649
*
- * if op == BAM_CMATCH:
- * o = min( pos + l, end) - max( pos, start ) # <<<<<<<<<<<<<<
- * if o > 0: overlap += o
- *
- */
- __pyx_t_4 = __pyx_v_end;
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_1) {
- __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_3 = __pyx_t_7;
- __pyx_t_7 = 0;
- } else {
- __Pyx_INCREF(__pyx_t_5);
- __pyx_t_3 = __pyx_t_5;
- }
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __pyx_v_start;
- __pyx_t_8 = __pyx_v_pos;
- if ((__pyx_t_4 > __pyx_t_8)) {
- __pyx_t_9 = __pyx_t_4;
- } else {
- __pyx_t_9 = __pyx_t_8;
- }
- __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyNumber_Subtract(__pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_v_o = __pyx_t_10;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2534
- * if op == BAM_CMATCH:
- * o = min( pos + l, end) - max( pos, start )
- * if o > 0: overlap += o # <<<<<<<<<<<<<<
+ * # get location of new data
+ * s = bam1_aux( src ) # <<<<<<<<<<<<<<
*
- * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ * # check if there is direct path from buffer.raw to tmp
*/
- __pyx_t_1 = (__pyx_v_o > 0);
- if (__pyx_t_1) {
- __pyx_v_overlap += __pyx_v_o;
- goto __pyx_L10;
- }
- __pyx_L10:;
- goto __pyx_L9;
- }
- __pyx_L9:;
+ __pyx_v_s = bam1_aux(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2536
- * if o > 0: overlap += o
+ /* "csamtools.pyx":2652
*
- * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
- * pos += l
+ * # check if there is direct path from buffer.raw to tmp
+ * temp = buffer.raw # <<<<<<<<<<<<<<
+ * memcpy( s, temp, total_size )
*
*/
- switch (__pyx_v_op) {
- case 0:
- case 2:
- case 3:
+ if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_14 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_18 = PyBytes_AsString(__pyx_t_14); if (unlikely((!__pyx_t_18) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_v_temp = __pyx_t_18;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2537
- *
- * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
- * pos += l # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2653
+ * # check if there is direct path from buffer.raw to tmp
+ * temp = buffer.raw
+ * memcpy( s, temp, total_size ) # <<<<<<<<<<<<<<
*
- * return overlap
+ * property flag:
*/
- __pyx_t_9 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_l); if (unlikely((__pyx_t_9 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_pos += __pyx_t_9;
- break;
- }
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ memcpy(__pyx_v_s, __pyx_v_temp, __pyx_t_16);
+ goto __pyx_L20;
}
+ __pyx_L20:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2539
- * pos += l
- *
- * return overlap # <<<<<<<<<<<<<<
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_t_14);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tags.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_fmts);
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_pytag);
+ __Pyx_XDECREF(__pyx_v_value);
+ __Pyx_XDECREF(__pyx_v_t);
+ __Pyx_XDECREF(__pyx_v_pytype);
+ __Pyx_XDECREF(__pyx_v_datafmt);
+ __Pyx_XDECREF(__pyx_v_datatype);
+ __Pyx_XDECREF(__pyx_v_mi);
+ __Pyx_XDECREF(__pyx_v_ma);
+ __Pyx_XDECREF(__pyx_v_absmax);
+ __Pyx_XDECREF(__pyx_v_fmt);
+ __Pyx_XDECREF(__pyx_v_total_size);
+ __Pyx_XDECREF(__pyx_v_buffer);
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4flag___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2657
+ * property flag:
+ * """properties flag"""
+ * def __get__(self): return self._delegate.core.flag # <<<<<<<<<<<<<<
+ * def __set__(self, flag): self._delegate.core.flag = flag
*
- * def opt(self, tag):
*/
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2657);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_overlap); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_AddTraceback("csamtools.AlignedRead.overlap");
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.AlignedRead.flag.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_l);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2541
- * return overlap
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_flag));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2658
+ * """properties flag"""
+ * def __get__(self): return self._delegate.core.flag
+ * def __set__(self, flag): self._delegate.core.flag = flag # <<<<<<<<<<<<<<
*
- * def opt(self, tag): # <<<<<<<<<<<<<<
- * """retrieves optional data given a two-letter *tag*"""
- * #see bam_aux.c: bam_aux_get() and bam_aux2i() etc
+ * property rname:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
- uint8_t *__pyx_v_v;
- PyObject *__pyx_v_type;
- PyObject *__pyx_r = NULL;
- char *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
- int __pyx_t_6;
- int __pyx_t_7;
- int __pyx_t_8;
+static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ uint32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("opt");
- __Pyx_TraceCall("opt", __pyx_f[0], 2541);
- __pyx_v_type = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2545
- * #see bam_aux.c: bam_aux_get() and bam_aux2i() etc
- * cdef uint8_t * v
- * v = bam_aux_get(self._delegate, tag) # <<<<<<<<<<<<<<
- * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
- * type = chr(v[0])
- */
- __pyx_t_1 = PyBytes_AsString(__pyx_v_tag); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_v = bam_aux_get(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate, __pyx_t_1);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2546
- * cdef uint8_t * v
- * v = bam_aux_get(self._delegate, tag)
- * if v == NULL: raise KeyError( "tag '%s' not present" % tag ) # <<<<<<<<<<<<<<
- * type = chr(v[0])
- * if type == 'c' or type == 'C' or type == 's' or type == 'S':
- */
- __pyx_t_2 = (__pyx_v_v == NULL);
- if (__pyx_t_2) {
- __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_75), __pyx_v_tag); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_KeyError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2547
- * v = bam_aux_get(self._delegate, tag)
- * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
- * type = chr(v[0]) # <<<<<<<<<<<<<<
- * if type == 'c' or type == 'C' or type == 's' or type == 'S':
- * return <int>bam_aux2i(v)
- */
- __pyx_t_3 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_chr, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_type);
- __pyx_v_type = __pyx_t_3;
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2548
- * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
- * type = chr(v[0])
- * if type == 'c' or type == 'C' or type == 's' or type == 'S': # <<<<<<<<<<<<<<
- * return <int>bam_aux2i(v)
- * elif type == 'i' or type == 'I':
- */
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__c), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__C), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_5) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__s), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_6) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__S), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __pyx_t_7;
- } else {
- __pyx_t_8 = __pyx_t_6;
- }
- __pyx_t_6 = __pyx_t_8;
- } else {
- __pyx_t_6 = __pyx_t_5;
- }
- __pyx_t_5 = __pyx_t_6;
- } else {
- __pyx_t_5 = __pyx_t_2;
- }
- if (__pyx_t_5) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2549
- * type = chr(v[0])
- * if type == 'c' or type == 'C' or type == 's' or type == 'S':
- * return <int>bam_aux2i(v) # <<<<<<<<<<<<<<
- * elif type == 'i' or type == 'I':
- * return <int32_t>bam_aux2i(v)
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2550
- * if type == 'c' or type == 'C' or type == 's' or type == 'S':
- * return <int>bam_aux2i(v)
- * elif type == 'i' or type == 'I': # <<<<<<<<<<<<<<
- * return <int32_t>bam_aux2i(v)
- * elif type == 'f' or type == 'F':
- */
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__i), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_5) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__I), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __pyx_t_2;
- } else {
- __pyx_t_6 = __pyx_t_5;
- }
- if (__pyx_t_6) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2551
- * return <int>bam_aux2i(v)
- * elif type == 'i' or type == 'I':
- * return <int32_t>bam_aux2i(v) # <<<<<<<<<<<<<<
- * elif type == 'f' or type == 'F':
- * return <float>bam_aux2f(v)
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __Pyx_PyInt_to_py_int32_t(bam_aux2i(__pyx_v_v)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2658);
+ __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_flag); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.flag = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2552
- * elif type == 'i' or type == 'I':
- * return <int32_t>bam_aux2i(v)
- * elif type == 'f' or type == 'F': # <<<<<<<<<<<<<<
- * return <float>bam_aux2f(v)
- * elif type == 'd' or type == 'D':
- */
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__f), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_6) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__F), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_2 = __pyx_t_5;
- } else {
- __pyx_t_2 = __pyx_t_6;
- }
- if (__pyx_t_2) {
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.flag.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2553
- * return <int32_t>bam_aux2i(v)
- * elif type == 'f' or type == 'F':
- * return <float>bam_aux2f(v) # <<<<<<<<<<<<<<
- * elif type == 'd' or type == 'D':
- * return <double>bam_aux2d(v)
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyFloat_FromDouble(bam_aux2f(__pyx_v_v)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rname___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2554
- * elif type == 'f' or type == 'F':
- * return <float>bam_aux2f(v)
- * elif type == 'd' or type == 'D': # <<<<<<<<<<<<<<
- * return <double>bam_aux2d(v)
- * elif type == 'A':
+/* "csamtools.pyx":2676
+ *
+ * """
+ * def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
+ * def __set__(self, tid): self._delegate.core.tid = tid
+ *
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__d), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__D), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = __pyx_t_6;
- } else {
- __pyx_t_5 = __pyx_t_2;
- }
- if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2555
- * return <float>bam_aux2f(v)
- * elif type == 'd' or type == 'D':
- * return <double>bam_aux2d(v) # <<<<<<<<<<<<<<
- * elif type == 'A':
- * # there might a more efficient way
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyFloat_FromDouble(bam_aux2d(__pyx_v_v)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2676);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2556
- * elif type == 'd' or type == 'D':
- * return <double>bam_aux2d(v)
- * elif type == 'A': # <<<<<<<<<<<<<<
- * # there might a more efficient way
- * # to convert a char into a string
- */
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_5) {
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.AlignedRead.rname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2559
- * # there might a more efficient way
- * # to convert a char into a string
- * return '%c' % <char>bam_aux2A(v) # <<<<<<<<<<<<<<
- * elif type == 'Z':
- * return <char*>bam_aux2Z(v)
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(bam_aux2A(__pyx_v_v)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_62), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_r = ((PyObject *)__pyx_t_4);
- __pyx_t_4 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2560
- * # to convert a char into a string
- * return '%c' % <char>bam_aux2A(v)
- * elif type == 'Z': # <<<<<<<<<<<<<<
- * return <char*>bam_aux2Z(v)
+/* "csamtools.pyx":2677
+ * """
+ * def __get__(self): return self._delegate.core.tid
+ * def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
*
+ * property tid:
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__Z), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2561
- * return '%c' % <char>bam_aux2A(v)
- * elif type == 'Z':
- * return <char*>bam_aux2Z(v) # <<<<<<<<<<<<<<
- *
- * def fancy_str (self):
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = PyBytes_FromString(bam_aux2Z(__pyx_v_v)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_r = ((PyObject *)__pyx_t_4);
- __pyx_t_4 = 0;
- goto __pyx_L0;
- goto __pyx_L6;
- }
- __pyx_L6:;
+static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2677);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.tid = __pyx_t_1;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.AlignedRead.opt");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.rname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_type);
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3tid___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2563
- * return <char*>bam_aux2Z(v)
+/* "csamtools.pyx":2690
*
- * def fancy_str (self): # <<<<<<<<<<<<<<
- * """returns list of fieldnames/values in pretty format for debugging
* """
+ * def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
+ * def __set__(self, tid): self._delegate.core.tid = tid
+ *
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_v_ret_string;
- PyObject *__pyx_v_field_names;
- PyObject *__pyx_v_fields_names_in_order;
- PyObject *__pyx_v_f;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- Py_ssize_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- int __pyx_t_10;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fancy_str");
- __Pyx_TraceCall("fancy_str", __pyx_f[0], 2563);
- __pyx_v_ret_string = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_field_names = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_fields_names_in_order = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
- __pyx_v_f = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2566
- * """returns list of fieldnames/values in pretty format for debugging
- * """
- * ret_string = [] # <<<<<<<<<<<<<<
- * field_names = {
- * "tid": "Contig index",
- */
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_ret_string));
- __pyx_v_ret_string = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2567
- * """
- * ret_string = []
- * field_names = { # <<<<<<<<<<<<<<
- * "tid": "Contig index",
- * "pos": "Mapped position on contig",
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__tid), ((PyObject *)__pyx_kp_s_76)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_kp_s_77)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mtid), ((PyObject *)__pyx_kp_s_78)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mpos), ((PyObject *)__pyx_kp_s_79)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__isize), ((PyObject *)__pyx_kp_s_80)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__flag), ((PyObject *)__pyx_kp_s_81)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__n_cigar), ((PyObject *)__pyx_kp_s_82)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__cigar), ((PyObject *)__pyx_kp_s_83)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_kp_s_84)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bin), ((PyObject *)__pyx_kp_s_85)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qname), ((PyObject *)__pyx_kp_s_86)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qname), ((PyObject *)__pyx_kp_s_87)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qseq), ((PyObject *)__pyx_kp_s_88)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qseq), ((PyObject *)__pyx_kp_s_89)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bqual), ((PyObject *)__pyx_kp_s_90)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_aux), ((PyObject *)__pyx_kp_s_91)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__m_data), ((PyObject *)__pyx_kp_s_92)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__data_len), ((PyObject *)__pyx_kp_s_93)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_v_field_names));
- __pyx_v_field_names = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2587
- * "data_len": "Current data length",
- * }
- * fields_names_in_order = ["tid", "pos", "mtid", "mpos", "isize", "flag", # <<<<<<<<<<<<<<
- * "n_cigar", "cigar", "qual", "bin", "l_qname", "qname",
- * "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
- */
- __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__tid));
- PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tid));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__tid));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__pos));
- PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__pos));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__mtid));
- PyList_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__mtid));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__mtid));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__mpos));
- PyList_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__mpos));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__mpos));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__isize));
- PyList_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__isize));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__isize));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__flag));
- PyList_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__flag));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__flag));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n_cigar));
- PyList_SET_ITEM(__pyx_t_1, 6, ((PyObject *)__pyx_n_s__n_cigar));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n_cigar));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__cigar));
- PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__cigar));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cigar));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__qual));
- PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__qual));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qual));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__bin));
- PyList_SET_ITEM(__pyx_t_1, 9, ((PyObject *)__pyx_n_s__bin));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__bin));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__l_qname));
- PyList_SET_ITEM(__pyx_t_1, 10, ((PyObject *)__pyx_n_s__l_qname));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l_qname));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__qname));
- PyList_SET_ITEM(__pyx_t_1, 11, ((PyObject *)__pyx_n_s__qname));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qname));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__l_qseq));
- PyList_SET_ITEM(__pyx_t_1, 12, ((PyObject *)__pyx_n_s__l_qseq));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l_qseq));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__qseq));
- PyList_SET_ITEM(__pyx_t_1, 13, ((PyObject *)__pyx_n_s__qseq));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qseq));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__bqual));
- PyList_SET_ITEM(__pyx_t_1, 14, ((PyObject *)__pyx_n_s__bqual));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__bqual));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__l_aux));
- PyList_SET_ITEM(__pyx_t_1, 15, ((PyObject *)__pyx_n_s__l_aux));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l_aux));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__m_data));
- PyList_SET_ITEM(__pyx_t_1, 16, ((PyObject *)__pyx_n_s__m_data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__m_data));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__data_len));
- PyList_SET_ITEM(__pyx_t_1, 17, ((PyObject *)__pyx_n_s__data_len));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data_len));
- __Pyx_DECREF(((PyObject *)__pyx_v_fields_names_in_order));
- __pyx_v_fields_names_in_order = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2591
- * "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
- *
- * for f in fields_names_in_order: # <<<<<<<<<<<<<<
- * if not f in self.__dict__:
- * continue
- */
- if (likely(((PyObject *)__pyx_v_fields_names_in_order) != Py_None)) {
- __pyx_t_2 = 0; __pyx_t_1 = ((PyObject *)__pyx_v_fields_names_in_order); __Pyx_INCREF(__pyx_t_1);
- } else {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- for (;;) {
- if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
- __Pyx_DECREF(__pyx_v_f);
- __pyx_v_f = __pyx_t_3;
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2592
- *
- * for f in fields_names_in_order:
- * if not f in self.__dict__: # <<<<<<<<<<<<<<
- * continue
- * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
- */
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = ((PySequence_Contains(__pyx_t_3, __pyx_v_f))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = (!__pyx_t_4);
- if (__pyx_t_5) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2593
- * for f in fields_names_in_order:
- * if not f in self.__dict__:
- * continue # <<<<<<<<<<<<<<
- * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
- *
- */
- goto __pyx_L5_continue;
- goto __pyx_L7;
- }
- __pyx_L7:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2594
- * if not f in self.__dict__:
- * continue
- * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f))) # <<<<<<<<<<<<<<
- *
- * for f in self.__dict__:
- */
- if (unlikely(__pyx_v_ret_string == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_field_names), __pyx_v_f); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_kp_s_95), __pyx_v_f); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyNumber_Add(__pyx_t_6, ((PyObject *)__pyx_kp_s_96)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
- __Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_9 = PyObject_Call(__pyx_t_6, __pyx_t_8, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_3 = 0;
- __pyx_t_7 = 0;
- __pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_94), __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_10 = PyList_Append(((PyObject *)__pyx_v_ret_string), ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_L5_continue:;
- }
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2596
- * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
- *
- * for f in self.__dict__: # <<<<<<<<<<<<<<
- * if not f in field_names:
- * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
- __pyx_t_2 = 0; __pyx_t_9 = __pyx_t_1; __Pyx_INCREF(__pyx_t_9);
- } else {
- __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- }
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- for (;;) {
- if (likely(PyList_CheckExact(__pyx_t_9))) {
- if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
- } else if (likely(PyTuple_CheckExact(__pyx_t_9))) {
- if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
- } else {
- __pyx_t_1 = PyIter_Next(__pyx_t_9);
- if (!__pyx_t_1) {
- if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- break;
- }
- __Pyx_GOTREF(__pyx_t_1);
- }
- __Pyx_DECREF(__pyx_v_f);
- __pyx_v_f = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2597
- *
- * for f in self.__dict__:
- * if not f in field_names: # <<<<<<<<<<<<<<
- * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
- * return ret_string
- */
- if (unlikely(((PyObject *)__pyx_v_field_names) == Py_None)) {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- } else {
- __pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = (!__pyx_t_5);
- if (__pyx_t_4) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2598
- * for f in self.__dict__:
- * if not f in field_names:
- * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f))) # <<<<<<<<<<<<<<
- * return ret_string
- *
- */
- if (unlikely(__pyx_v_ret_string == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
- __Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_7 = PyObject_Call(__pyx_t_1, __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
- __Pyx_GIVEREF(__pyx_v_f);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_8));
- PyTuple_SET_ITEM(__pyx_t_8, 1, ((PyObject *)__pyx_kp_s_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_8));
- PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_94), __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_10 = PyList_Append(((PyObject *)__pyx_v_ret_string), ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L10;
- }
- __pyx_L10:;
- }
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2599
- * if not f in field_names:
- * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
- * return ret_string # <<<<<<<<<<<<<<
- *
- * cdef class PileupProxy:
- */
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2690);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_ret_string));
- __pyx_r = ((PyObject *)__pyx_v_ret_string);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("csamtools.AlignedRead.fancy_str");
+ __Pyx_AddTraceback("csamtools.AlignedRead.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_ret_string);
- __Pyx_DECREF(__pyx_v_field_names);
- __Pyx_DECREF(__pyx_v_fields_names_in_order);
- __Pyx_DECREF(__pyx_v_f);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2623
- * cdef int n_pu
- *
- * def __init__(self): # <<<<<<<<<<<<<<
- * raise TypeError("This class cannot be instantiated from Python")
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2691
+ * """
+ * def __get__(self): return self._delegate.core.tid
+ * def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
*
+ * property pos:
*/
-static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 2623);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2624
- *
- * def __init__(self):
- * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
- *
- * def __str__(self):
- */
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_97));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_97));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_97));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_TypeError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2691);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.PileupProxy.__init__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.tid.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2626
- * raise TypeError("This class cannot be instantiated from Python")
- *
- * def __str__(self): # <<<<<<<<<<<<<<
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" +\
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3pos___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2695
+ * property pos:
+ * """0-based leftmost coordinate"""
+ * def __get__(self): return self._delegate.core.pos # <<<<<<<<<<<<<<
+ * def __set__(self, pos):
+ * ## setting the cigar string also updates the "bin" attribute
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy___str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy___str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 2626);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2627
- *
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
- * "\n" +\
- * "\n".join( map(str, self.pileups) )
- */
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2695);
__Pyx_XDECREF(__pyx_r);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2628
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" +\ # <<<<<<<<<<<<<<
- * "\n".join( map(str, self.pileups) )
- *
- */
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2627
- *
- * def __str__(self):
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
- * "\n" +\
- * "\n".join( map(str, self.pileups) )
- */
- __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_map, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2629
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" +\
- * "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
- *
- * property tid:
- */
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_map, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_5, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Add(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.PileupProxy.__str__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2633
- * property tid:
- * '''the chromosome ID as is defined in the header'''
- * def __get__(self): return self.tid # <<<<<<<<<<<<<<
- *
- * property n:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_pos));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2696
+ * """0-based leftmost coordinate"""
+ * def __get__(self): return self._delegate.core.pos
+ * def __set__(self, pos): # <<<<<<<<<<<<<<
+ * ## setting the cigar string also updates the "bin" attribute
+ * cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos) {
+ bam1_t *__pyx_v_src;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2633);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2696);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2699
+ * ## setting the cigar string also updates the "bin" attribute
+ * cdef bam1_t * src
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.core.n_cigar:
+ * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
+
+ /* "csamtools.pyx":2700
+ * cdef bam1_t * src
+ * src = self._delegate
+ * if src.core.n_cigar: # <<<<<<<<<<<<<<
+ * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
+ * else:
+ */
+ if (__pyx_v_src->core.n_cigar) {
+
+ /* "csamtools.pyx":2701
+ * src = self._delegate
+ * if src.core.n_cigar:
+ * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) ) # <<<<<<<<<<<<<<
+ * else:
+ * src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
+ */
+ __pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)));
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2703
+ * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
+ * else:
+ * src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1) # <<<<<<<<<<<<<<
+ * self._delegate.core.pos = pos
+ * property bin:
+ */
+ __pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, (__pyx_v_src->core.pos + 1));
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2704
+ * else:
+ * src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
+ * self._delegate.core.pos = pos # <<<<<<<<<<<<<<
+ * property bin:
+ * """properties bin"""
+ */
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.pos = __pyx_t_1;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.tid.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.pos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2637
- * property n:
- * '''number of reads mapping to this column.'''
- * def __get__(self): return self.n_pu # <<<<<<<<<<<<<<
- * def __set__(self, n): self.n_pu = n
- *
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3bin___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2707
+ * property bin:
+ * """properties bin"""
+ * def __get__(self): return self._delegate.core.bin # <<<<<<<<<<<<<<
+ * def __set__(self, bin): self._delegate.core.bin = bin
+ * property rlen:
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2637);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2707);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.n.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.bin.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2638
- * '''number of reads mapping to this column.'''
- * def __get__(self): return self.n_pu
- * def __set__(self, n): self.n_pu = n # <<<<<<<<<<<<<<
- *
- * property pos:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_bin));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2708
+ * """properties bin"""
+ * def __get__(self): return self._delegate.core.bin
+ * def __set__(self, bin): self._delegate.core.bin = bin # <<<<<<<<<<<<<<
+ * property rlen:
+ * '''length of the read (read only). Returns 0 if not given.'''
*/
-static int __pyx_pf_9csamtools_11PileupProxy_1n___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
-static int __pyx_pf_9csamtools_11PileupProxy_1n___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
+static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin) {
int __pyx_r;
- int __pyx_t_1;
+ __Pyx_RefNannyDeclarations
+ uint32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2638);
- __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_n); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2638; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2708);
+ __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_bin); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.bin = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.PileupProxy.n.__set__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.bin.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2641
- *
- * property pos:
- * def __get__(self): return self.pos # <<<<<<<<<<<<<<
- *
- * property pileups:
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2711
+ * property rlen:
+ * '''length of the read (read only). Returns 0 if not given.'''
+ * def __get__(self): return self._delegate.core.l_qseq # <<<<<<<<<<<<<<
+ * property aend:
+ * '''aligned reference position of the read on the reference genome.
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2641);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2711);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.pos.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.rlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2645
- * property pileups:
- * '''list of reads (:class:`pysam.PileupRead`) aligned to this column'''
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4aend___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2717
+ * aend points to one past the last aligned residue.
+ * Returns None if not available.'''
* def __get__(self): # <<<<<<<<<<<<<<
- * cdef int x
- * pileups = []
+ * cdef bam1_t * src
+ * src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self) {
- int __pyx_v_x;
- PyObject *__pyx_v_pileups;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
+ PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2645);
- __pyx_v_pileups = ((PyObject *)Py_None); __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2717);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2647
+ /* "csamtools.pyx":2719
* def __get__(self):
- * cdef int x
- * pileups = [] # <<<<<<<<<<<<<<
- * # warning: there could be problems if self.n and self.buf are
- * # out of sync.
+ * cdef bam1_t * src
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
+ * return None
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_v_pileups));
- __pyx_v_pileups = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2650
- * # warning: there could be problems if self.n and self.buf are
- * # out of sync.
- * for x from 0 <= x < self.n_pu: # <<<<<<<<<<<<<<
- * pileups.append( makePileupRead( &(self.plp[x])) )
- * return pileups
+ /* "csamtools.pyx":2720
+ * cdef bam1_t * src
+ * src = self._delegate
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
+ * return None
+ * return bam_calend(&src.core, bam1_cigar(src))
*/
- __pyx_t_2 = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu;
- for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) {
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (!__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_3;
+ }
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2651
- * # out of sync.
- * for x from 0 <= x < self.n_pu:
- * pileups.append( makePileupRead( &(self.plp[x])) ) # <<<<<<<<<<<<<<
- * return pileups
+ /* "csamtools.pyx":2721
+ * src = self._delegate
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
+ * return None # <<<<<<<<<<<<<<
+ * return bam_calend(&src.core, bam1_cigar(src))
*
*/
- if (unlikely(__pyx_v_pileups == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyList_Append(((PyObject *)__pyx_v_pileups), __pyx_t_1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
}
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2652
- * for x from 0 <= x < self.n_pu:
- * pileups.append( makePileupRead( &(self.plp[x])) )
- * return pileups # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2722
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
+ * return None
+ * return bam_calend(&src.core, bam1_cigar(src)) # <<<<<<<<<<<<<<
*
- * cdef class PileupRead:
+ * property alen:
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_pileups));
- __pyx_r = ((PyObject *)__pyx_v_pileups);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.pileups.__get__");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.aend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_pileups);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2667
- * uint32_t _is_tail
- *
- * def __init__(self): # <<<<<<<<<<<<<<
- * raise TypeError("This class cannot be instantiated from Python")
- *
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4alen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2727
+ * '''aligned length of the read on the reference genome. Returns None if
+ * not available.'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef bam1_t * src
+ * src = self._delegate
*/
-static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 2667);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2727);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2668
- *
- * def __init__(self):
- * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
- *
- * def __str__(self):
+ /* "csamtools.pyx":2729
+ * def __get__(self):
+ * cdef bam1_t * src
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
+ * return None
+ */
+ __pyx_v_src = __pyx_v_self->_delegate;
+
+ /* "csamtools.pyx":2730
+ * cdef bam1_t * src
+ * src = self._delegate
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
+ * return None
+ * return bam_calend(&src.core,
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_97));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_97));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_97));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_TypeError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.PileupRead.__init__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ if (!__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
+ __pyx_t_5 = __pyx_t_4;
+ } else {
+ __pyx_t_5 = __pyx_t_3;
+ }
+ if (__pyx_t_5) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2670
- * raise TypeError("This class cannot be instantiated from Python")
- *
- * def __str__(self): # <<<<<<<<<<<<<<
- * return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) )
- *
+ /* "csamtools.pyx":2731
+ * src = self._delegate
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
+ * return None # <<<<<<<<<<<<<<
+ * return bam_calend(&src.core,
+ * bam1_cigar(src)) - \
*/
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(Py_None);
+ __pyx_r = Py_None;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
-static PyObject *__pyx_pf_9csamtools_10PileupRead___str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead___str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 2670);
+ /* "csamtools.pyx":2732
+ * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
+ * return None
+ * return bam_calend(&src.core, # <<<<<<<<<<<<<<
+ * bam1_cigar(src)) - \
+ * self._delegate.core.pos
+ */
+ __Pyx_XDECREF(__pyx_r);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2671
- *
- * def __str__(self):
- * return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2734
+ * return bam_calend(&src.core,
+ * bam1_cigar(src)) - \
+ * self._delegate.core.pos # <<<<<<<<<<<<<<
*
- * property alignment:
+ * property mapq:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - __pyx_v_self->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_9, 3, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_9, 4, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_9, 5, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_9, 6, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_7 = 0;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_map, __pyx_t_8, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_1, __pyx_t_8, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_r = __pyx_t_9;
- __pyx_t_9 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("csamtools.PileupRead.__str__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.alen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2675
- * property alignment:
- * """a :class:`pysam.AlignedRead` object of the aligned read"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._alignment
- * property qpos:
- */
-
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2675);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2676
- * """a :class:`pysam.AlignedRead` object of the aligned read"""
- * def __get__(self):
- * return self._alignment # <<<<<<<<<<<<<<
- * property qpos:
- * """position of the read base at the pileup site, 0-based"""
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment));
- __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment);
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2679
- * property qpos:
- * """position of the read base at the pileup site, 0-based"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._qpos
- * property indel:
+/* "csamtools.pyx":2738
+ * property mapq:
+ * """mapping quality"""
+ * def __get__(self): return self._delegate.core.qual # <<<<<<<<<<<<<<
+ * def __set__(self, qual): self._delegate.core.qual = qual
+ *
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2679);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2680
- * """position of the read base at the pileup site, 0-based"""
- * def __get__(self):
- * return self._qpos # <<<<<<<<<<<<<<
- * property indel:
- * """indel length; 0 for no indel, positive for ins and negative for del"""
- */
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2738);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.qpos.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2683
- * property indel:
- * """indel length; 0 for no indel, positive for ins and negative for del"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._indel
- * property is_del:
- */
-
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2739
+ * """mapping quality"""
+ * def __get__(self): return self._delegate.core.qual
+ * def __set__(self, qual): self._delegate.core.qual = qual # <<<<<<<<<<<<<<
+ *
+ * property mrnm:
+ */
+
+static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ uint32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2683);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2739);
+ __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.qual = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2684
- * """indel length; 0 for no indel, positive for ins and negative for del"""
- * def __get__(self):
- * return self._indel # <<<<<<<<<<<<<<
- * property is_del:
- * """1 iff the base on the padded read is a deletion"""
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2745
+ * deprecated, use RNEXT instead.
+ * """
+ * def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
+ * def __set__(self, mtid): self._delegate.core.mtid = mtid
+ * property rnext:
*/
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2745);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.indel.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2687
- * property is_del:
- * """1 iff the base on the padded read is a deletion"""
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._is_del
- * property is_head:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2746
+ * """
+ * def __get__(self): return self._delegate.core.mtid
+ * def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
+ * property rnext:
+ * """the :term:`reference` id of the mate """
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2687);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2746);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2688
- * """1 iff the base on the padded read is a deletion"""
- * def __get__(self):
- * return self._is_del # <<<<<<<<<<<<<<
- * property is_head:
- * def __get__(self):
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2749
+ * property rnext:
+ * """the :term:`reference` id of the mate """
+ * def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
+ * def __set__(self, mtid): self._delegate.core.mtid = mtid
+ * property mpos:
*/
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2749);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.is_del.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.rnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2690
- * return self._is_del
- * property is_head:
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._is_head
- * property is_tail:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2750
+ * """the :term:`reference` id of the mate """
+ * def __get__(self): return self._delegate.core.mtid
+ * def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
+ * property mpos:
+ * """the position of the mate
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2690);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2750);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2691
- * property is_head:
- * def __get__(self):
- * return self._is_head # <<<<<<<<<<<<<<
- * property is_tail:
- * def __get__(self):
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.rnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2754
+ * """the position of the mate
+ * deprecated, use PNEXT instead."""
+ * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos
+ * property pnext:
*/
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2754);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.is_head.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2693
- * return self._is_head
- * property is_tail:
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._is_tail
- * property level:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2755
+ * deprecated, use PNEXT instead."""
+ * def __get__(self): return self._delegate.core.mpos
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
+ * property pnext:
+ * """the position of the mate"""
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2693);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2755);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2694
- * property is_tail:
- * def __get__(self):
- * return self._is_tail # <<<<<<<<<<<<<<
- * property level:
- * def __get__(self):
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2758
+ * property pnext:
+ * """the position of the mate"""
+ * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos
+ * property isize:
*/
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2758);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.is_tail.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.pnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2696
- * return self._is_tail
- * property level:
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._level
- *
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2759
+ * """the position of the mate"""
+ * def __get__(self): return self._delegate.core.mpos
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
+ * property isize:
+ * """the insert size
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2696);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2759);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2697
- * property level:
- * def __get__(self):
- * return self._level # <<<<<<<<<<<<<<
- *
- * class Outs:
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.pnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5isize___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2763
+ * """the insert size
+ * deprecated: use tlen instead"""
+ * def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
+ * def __set__(self, isize): self._delegate.core.isize = isize
+ * property tlen:
*/
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2763);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.level.__get__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.isize.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2701
- * class Outs:
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1): # <<<<<<<<<<<<<<
- * self.streams = []
- * self.id = id
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2764
+ * deprecated: use tlen instead"""
+ * def __get__(self): return self._delegate.core.isize
+ * def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
+ * property tlen:
+ * """the insert size"""
*/
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_4Outs___init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs___init__)};
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_self = 0;
- PyObject *__pyx_v_id = 0;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
+static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 2701);
- __pyx_self = __pyx_self;
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- values[1] = ((PyObject *)__pyx_int_1);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__id);
- if (value) { values[1] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2701; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_self = values[0];
- __pyx_v_id = values[1];
- } else {
- __pyx_v_id = ((PyObject *)__pyx_int_1);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: __pyx_v_id = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_self = PyTuple_GET_ITEM(__pyx_args, 0);
- break;
- default: goto __pyx_L5_argtuple_error;
- }
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2701; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.__init__");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2764);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.isize = __pyx_t_1;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2702
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1):
- * self.streams = [] # <<<<<<<<<<<<<<
- * self.id = id
- *
- */
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__streams, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2703
- * def __init__(self, id = 1):
- * self.streams = []
- * self.id = id # <<<<<<<<<<<<<<
- *
- * def setdevice(self, filename):
- */
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__id, __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Outs.__init__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.isize.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2705
- * self.id = id
- *
- * def setdevice(self, filename): # <<<<<<<<<<<<<<
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2767
+ * property tlen:
+ * """the insert size"""
+ * def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
+ * def __set__(self, isize): self._delegate.core.isize = isize
+ * property is_paired:
*/
-static PyObject *__pyx_pf_9csamtools_4Outs_setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pf_9csamtools_4Outs_setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_setdevice)};
-static PyObject *__pyx_pf_9csamtools_4Outs_setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_self = 0;
- PyObject *__pyx_v_filename = 0;
- PyObject *__pyx_v_fd;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setdevice");
- __Pyx_TraceCall("setdevice", __pyx_f[0], 2705);
- __pyx_self = __pyx_self;
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2705; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2705; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_self = values[0];
- __pyx_v_filename = values[1];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_self = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_filename = PyTuple_GET_ITEM(__pyx_args, 1);
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2705; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.setdevice");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_fd = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2707
- * def setdevice(self, filename):
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY) # <<<<<<<<<<<<<<
- * self.setfd(fd)
- *
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
- __Pyx_GIVEREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_fd);
- __pyx_v_fd = __pyx_t_3;
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2708
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
- * self.setfd(fd) # <<<<<<<<<<<<<<
- *
- * def setfile(self, filename):
- */
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2767);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_fd);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fd);
- __Pyx_GIVEREF(__pyx_v_fd);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Outs.setdevice");
+ __Pyx_AddTraceback("csamtools.AlignedRead.tlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_fd);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2710
- * self.setfd(fd)
- *
- * def setfile(self, filename): # <<<<<<<<<<<<<<
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2768
+ * """the insert size"""
+ * def __get__(self): return self._delegate.core.isize
+ * def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
+ * property is_paired:
+ * """true if read is paired in sequencing"""
*/
-static PyObject *__pyx_pf_9csamtools_4Outs_setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pf_9csamtools_4Outs_setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_setfile)};
-static PyObject *__pyx_pf_9csamtools_4Outs_setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_self = 0;
- PyObject *__pyx_v_filename = 0;
- PyObject *__pyx_v_fd;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfile");
- __Pyx_TraceCall("setfile", __pyx_f[0], 2710);
- __pyx_self = __pyx_self;
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_self = values[0];
- __pyx_v_filename = values[1];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_self = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_filename = PyTuple_GET_ITEM(__pyx_args, 1);
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.setfile");
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2768);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.isize = __pyx_t_1;
+
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.tlen.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_fd = Py_None; __Pyx_INCREF(Py_None);
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2712
- * def setfile(self, filename):
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660); # <<<<<<<<<<<<<<
- * self.setfd(fd)
- *
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_CREAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Or(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_filename);
- __Pyx_GIVEREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_int_0660);
- PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_int_0660);
- __Pyx_GIVEREF(__pyx_int_0660);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_fd);
- __pyx_v_fd = __pyx_t_1;
- __pyx_t_1 = 0;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2713
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
- * self.setfd(fd) # <<<<<<<<<<<<<<
- *
- * def setfd(self, fd):
+/* "csamtools.pyx":2771
+ * property is_paired:
+ * """true if read is paired in sequencing"""
+ * def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FPAIRED
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2771);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyBool_FromLong(((__pyx_v_self->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_v_fd);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_fd);
- __Pyx_GIVEREF(__pyx_v_fd);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.Outs.setfile");
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_fd);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2715
- * self.setfd(fd)
- *
- * def setfd(self, fd): # <<<<<<<<<<<<<<
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2772
+ * """true if read is paired in sequencing"""
+ * def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FPAIRED
+ * else: self._delegate.core.flag &= ~BAM_FPAIRED
*/
-static PyObject *__pyx_pf_9csamtools_4Outs_setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_setfd[] = "Outs.setfd(self, fd)";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pf_9csamtools_4Outs_setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_setfd)};
-static PyObject *__pyx_pf_9csamtools_4Outs_setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_self = 0;
- PyObject *__pyx_v_fd = 0;
- PyObject *__pyx_v_ofd;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
+static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfd");
- __Pyx_TraceCall("setfd", __pyx_f[0], 2715);
- __pyx_self = __pyx_self;
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fd);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2715; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2715; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_self = values[0];
- __pyx_v_fd = values[1];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_self = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_fd = PyTuple_GET_ITEM(__pyx_args, 1);
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2715; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.setfd");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_ofd = Py_None; __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2772);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2716
- *
- * def setfd(self, fd):
- * ofd = os.dup(self.id) # Save old stream on new unit. # <<<<<<<<<<<<<<
- * self.streams.append(ofd)
- * sys.stdout.flush() # Buffered data goes to old stream.
+ /* "csamtools.pyx":2773
+ * def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FPAIRED # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FPAIRED
+ * property is_proper_pair:
+ */
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1);
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2774
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FPAIRED
+ * else: self._delegate.core.flag &= ~BAM_FPAIRED # <<<<<<<<<<<<<<
+ * property is_proper_pair:
+ * """true if read is mapped in a proper pair"""
+ */
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1));
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2777
+ * property is_proper_pair:
+ * """true if read is mapped in a proper pair"""
+ * def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2777);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_ofd);
- __pyx_v_ofd = __pyx_t_1;
+ __pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2717
- * def setfd(self, fd):
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd) # <<<<<<<<<<<<<<
- * sys.stdout.flush() # Buffered data goes to old stream.
- * sys.stderr.flush() # Buffered data goes to old stream.
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2778
+ * """true if read is mapped in a proper pair"""
+ * def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
+ * else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_Append(__pyx_t_1, __pyx_v_ofd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2718
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
- * sys.stdout.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
- * sys.stderr.flush() # Buffered data goes to old stream.
- * os.dup2(fd, self.id) # Open unit 1 on new stream.
+static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2778);
+
+ /* "csamtools.pyx":2779
+ * def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
+ * property is_unmapped:
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 2);
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2719
- * self.streams.append(ofd)
- * sys.stdout.flush() # Buffered data goes to old stream.
- * sys.stderr.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
- * os.dup2(fd, self.id) # Open unit 1 on new stream.
- * os.close(fd) # Close other unit (look out, caller.)
+ /* "csamtools.pyx":2780
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
+ * else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
+ * property is_unmapped:
+ * """true if read itself is unmapped"""
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stderr); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~2));
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2720
- * sys.stdout.flush() # Buffered data goes to old stream.
- * sys.stderr.flush() # Buffered data goes to old stream.
- * os.dup2(fd, self.id) # Open unit 1 on new stream. # <<<<<<<<<<<<<<
- * os.close(fd) # Close other unit (look out, caller.)
- *
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2783
+ * property is_unmapped:
+ * """true if read itself is unmapped"""
+ * def __get__(self): return (self.flag & BAM_FUNMAP) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FUNMAP
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__dup2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2783);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_fd);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_fd);
- __Pyx_GIVEREF(__pyx_v_fd);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2721
- * sys.stderr.flush() # Buffered data goes to old stream.
- * os.dup2(fd, self.id) # Open unit 1 on new stream.
- * os.close(fd) # Close other unit (look out, caller.) # <<<<<<<<<<<<<<
- *
- * def restore(self):
- */
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(__pyx_v_fd);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fd);
- __Pyx_GIVEREF(__pyx_v_fd);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Outs.setfd");
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_ofd);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2723
- * os.close(fd) # Close other unit (look out, caller.)
- *
- * def restore(self): # <<<<<<<<<<<<<<
- * '''restore previous output stream'''
- * if self.streams:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2784
+ * """true if read itself is unmapped"""
+ * def __get__(self): return (self.flag & BAM_FUNMAP) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FUNMAP
+ * else: self._delegate.core.flag &= ~BAM_FUNMAP
*/
-static PyObject *__pyx_pf_9csamtools_4Outs_restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_restore[] = "Outs.restore(self)\nrestore previous output stream";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pf_9csamtools_4Outs_restore, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_restore)};
-static PyObject *__pyx_pf_9csamtools_4Outs_restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("restore");
- __Pyx_TraceCall("restore", __pyx_f[0], 2723);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2784);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2725
- * def restore(self):
- * '''restore previous output stream'''
- * if self.streams: # <<<<<<<<<<<<<<
- * # the following was not sufficient, hence flush both stderr and stdout
- * # os.fsync( self.id )
+ /* "csamtools.pyx":2785
+ * def __get__(self): return (self.flag & BAM_FUNMAP) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FUNMAP # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FUNMAP
+ * property mate_is_unmapped:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 4);
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2728
- * # the following was not sufficient, hence flush both stderr and stdout
- * # os.fsync( self.id )
- * sys.stdout.flush() # <<<<<<<<<<<<<<
- * sys.stderr.flush()
- * os.dup2(self.streams[-1], self.id)
+ /* "csamtools.pyx":2786
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FUNMAP
+ * else: self._delegate.core.flag &= ~BAM_FUNMAP # <<<<<<<<<<<<<<
+ * property mate_is_unmapped:
+ * """true if the mate is unmapped"""
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stdout); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2729
- * # os.fsync( self.id )
- * sys.stdout.flush()
- * sys.stderr.flush() # <<<<<<<<<<<<<<
- * os.dup2(self.streams[-1], self.id)
- * os.close(self.streams[-1])
- */
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stderr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~4));
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2730
- * sys.stdout.flush()
- * sys.stderr.flush()
- * os.dup2(self.streams[-1], self.id) # <<<<<<<<<<<<<<
- * os.close(self.streams[-1])
- * del self.streams[-1]
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_4 = 0;
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2731
- * sys.stderr.flush()
- * os.dup2(self.streams[-1], self.id)
- * os.close(self.streams[-1]) # <<<<<<<<<<<<<<
- * del self.streams[-1]
- *
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_5, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2732
- * os.dup2(self.streams[-1], self.id)
- * os.close(self.streams[-1])
- * del self.streams[-1] # <<<<<<<<<<<<<<
- *
- * def _samtools_dispatch( method,
+/* "csamtools.pyx":2789
+ * property mate_is_unmapped:
+ * """true if the mate is unmapped"""
+ * def __get__(self): return (self.flag & BAM_FMUNMAP) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FMUNMAP
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_DelItemInt(__pyx_t_3, -1, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L5;
- }
- __pyx_L5:;
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2789);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.Outs.restore");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2734
- * del self.streams[-1]
- *
- * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
- * args = (),
- * catch_stdout = True,
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2790
+ * """true if the mate is unmapped"""
+ * def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FMUNMAP
+ * else: self._delegate.core.flag &= ~BAM_FMUNMAP
*/
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True, catch_stderr=False)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout and stderr to capture it \n from samtools. If for some reason stdout/stderr disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n \n .. note:: \n This method captures stdout and stderr using temporary files, \n which are then read into memory in their entirety. This method\n is slow and might cause large memory overhead. \n\n See http://bytes.com/topic/c/answers/487231-how-capture-stdout-temporarily\n on the topic of redirecting stderr/stdout.\n ";
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_method = 0;
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_catch_stdout = 0;
- PyObject *__pyx_v_catch_stderr = 0;
- PyObject *__pyx_v_stderr_h;
- PyObject *__pyx_v_stderr_f;
- PyObject *__pyx_v_stderr_save;
- PyObject *__pyx_v_stdout_h;
- PyObject *__pyx_v_stdout_f;
- PyObject *__pyx_v_stdout_save;
- char **__pyx_v_cargs;
- int __pyx_v_i;
- int __pyx_v_n;
- int __pyx_v_retval;
- PyObject *__pyx_v_out_stdout;
- PyObject *__pyx_v_out_stderr;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- Py_ssize_t __pyx_t_7;
- char *__pyx_t_8;
- int __pyx_t_9;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,&__pyx_n_s__catch_stderr,0};
+static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_samtools_dispatch");
- __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 2734);
- __pyx_self = __pyx_self;
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[4] = {0,0,0,0};
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2790);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2735
- *
- * def _samtools_dispatch( method,
- * args = (), # <<<<<<<<<<<<<<
- * catch_stdout = True,
- * catch_stderr = False,
+ /* "csamtools.pyx":2791
+ * def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FMUNMAP # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FMUNMAP
+ * property is_reverse:
*/
- values[1] = ((PyObject *)__pyx_empty_tuple);
- values[2] = __pyx_k_98;
- values[3] = __pyx_k_99;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__args);
- if (value) { values[1] = value; kw_args--; }
- }
- case 2:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__catch_stdout);
- if (value) { values[2] = value; kw_args--; }
- }
- case 3:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__catch_stderr);
- if (value) { values[3] = value; kw_args--; }
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2734; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_method = values[0];
- __pyx_v_args = values[1];
- __pyx_v_catch_stdout = values[2];
- __pyx_v_catch_stderr = values[3];
- } else {
- __pyx_v_args = ((PyObject *)__pyx_empty_tuple);
- __pyx_v_catch_stdout = __pyx_k_98;
- __pyx_v_catch_stderr = __pyx_k_99;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 4: __pyx_v_catch_stderr = PyTuple_GET_ITEM(__pyx_args, 3);
- case 3: __pyx_v_catch_stdout = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: __pyx_v_args = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: __pyx_v_method = PyTuple_GET_ITEM(__pyx_args, 0);
- break;
- default: goto __pyx_L5_argtuple_error;
- }
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 8);
+ goto __pyx_L3;
}
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2734; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools._samtools_dispatch");
+ /*else*/ {
+
+ /* "csamtools.pyx":2792
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FMUNMAP
+ * else: self._delegate.core.flag &= ~BAM_FMUNMAP # <<<<<<<<<<<<<<
+ * property is_reverse:
+ * """true if read is mapped to reverse strand"""
+ */
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~8));
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __Pyx_INCREF(__pyx_v_args);
- __pyx_v_stderr_h = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_stderr_f = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_stderr_save = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_stdout_h = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_stdout_f = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_stdout_save = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_out_stdout = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_out_stderr = Py_None; __Pyx_INCREF(Py_None);
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2762
- *
- * # some special cases
- * if method == "index": # <<<<<<<<<<<<<<
- * if not os.path.exists( args[0] ):
- * raise IOError( "No such file or directory: '%s'" % args[0] )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2795
+ * property is_reverse:
+ * """true if read is mapped to reverse strand"""
+ * def __get__(self): return (self.flag & BAM_FREVERSE) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREVERSE
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_method, ((PyObject *)__pyx_n_s__index), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2795);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2763
- * # some special cases
- * if method == "index":
- * if not os.path.exists( args[0] ): # <<<<<<<<<<<<<<
- * raise IOError( "No such file or directory: '%s'" % args[0] )
- *
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2796
+ * """true if read is mapped to reverse strand"""
+ * def __get__(self): return (self.flag & BAM_FREVERSE) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FREVERSE
+ * else: self._delegate.core.flag &= ~BAM_FREVERSE
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = (!__pyx_t_2);
- if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2764
- * if method == "index":
- * if not os.path.exists( args[0] ):
- * raise IOError( "No such file or directory: '%s'" % args[0] ) # <<<<<<<<<<<<<<
- *
- * # redirect stderr and stdout to file
- */
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_100), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
- }
- __pyx_L7:;
- goto __pyx_L6;
- }
- __pyx_L6:;
+static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2796);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2767
- *
- * # redirect stderr and stdout to file
- * if catch_stderr: # <<<<<<<<<<<<<<
- * stderr_h, stderr_f = tempfile.mkstemp()
- * stderr_save = Outs( sys.stderr.fileno() )
+ /* "csamtools.pyx":2797
+ * def __get__(self): return (self.flag & BAM_FREVERSE) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREVERSE # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FREVERSE
+ * property mate_is_reverse:
*/
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stderr); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_5) {
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 16);
+ goto __pyx_L3;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2768
- * # redirect stderr and stdout to file
- * if catch_stderr:
- * stderr_h, stderr_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
- * stderr_save = Outs( sys.stderr.fileno() )
- * stderr_save.setfd( stderr_h )
+ /* "csamtools.pyx":2798
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREVERSE
+ * else: self._delegate.core.flag &= ~BAM_FREVERSE # <<<<<<<<<<<<<<
+ * property mate_is_reverse:
+ * """true is read is mapped to reverse strand"""
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (PyTuple_CheckExact(__pyx_t_4) && likely(PyTuple_GET_SIZE(__pyx_t_4) == 2)) {
- PyObject* tuple = __pyx_t_4;
- __pyx_t_3 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_stderr_h);
- __pyx_v_stderr_h = __pyx_t_3;
- __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_stderr_f);
- __pyx_v_stderr_f = __pyx_t_1;
- __pyx_t_1 = 0;
- } else {
- __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_6, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_UnpackItem(__pyx_t_6, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_EndUnpack(__pyx_t_6, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_stderr_h);
- __pyx_v_stderr_h = __pyx_t_3;
- __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_stderr_f);
- __pyx_v_stderr_f = __pyx_t_1;
- __pyx_t_1 = 0;
- }
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~16));
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2769
- * if catch_stderr:
- * stderr_h, stderr_f = tempfile.mkstemp()
- * stderr_save = Outs( sys.stderr.fileno() ) # <<<<<<<<<<<<<<
- * stderr_save.setfd( stderr_h )
- *
- */
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stderr); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__fileno); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_4, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_stderr_save);
- __pyx_v_stderr_save = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2770
- * stderr_h, stderr_f = tempfile.mkstemp()
- * stderr_save = Outs( sys.stderr.fileno() )
- * stderr_save.setfd( stderr_h ) # <<<<<<<<<<<<<<
- *
- * if catch_stdout:
- */
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_stderr_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_stderr_h);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_stderr_h);
- __Pyx_GIVEREF(__pyx_v_stderr_h);
- __pyx_t_4 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L8;
- }
- __pyx_L8:;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2772
- * stderr_save.setfd( stderr_h )
- *
- * if catch_stdout: # <<<<<<<<<<<<<<
- * stdout_h, stdout_f = tempfile.mkstemp()
- * stdout_save = Outs( sys.stdout.fileno() )
+/* "csamtools.pyx":2801
+ * property mate_is_reverse:
+ * """true is read is mapped to reverse strand"""
+ * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FMREVERSE
*/
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2773
- *
- * if catch_stdout:
- * stdout_h, stdout_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
- * stdout_save = Outs( sys.stdout.fileno() )
- * stdout_save.setfd( stdout_h )
- */
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyTuple_CheckExact(__pyx_t_4) && likely(PyTuple_GET_SIZE(__pyx_t_4) == 2)) {
- PyObject* tuple = __pyx_t_4;
- __pyx_t_1 = PyTuple_GET_ITEM(tuple, 0); __Pyx_INCREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_GET_ITEM(tuple, 1); __Pyx_INCREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_stdout_h);
- __pyx_v_stdout_h = __pyx_t_1;
- __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_stdout_f);
- __pyx_v_stdout_f = __pyx_t_3;
- __pyx_t_3 = 0;
- } else {
- __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_1 = __Pyx_UnpackItem(__pyx_t_6, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_6, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_EndUnpack(__pyx_t_6, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_v_stdout_h);
- __pyx_v_stdout_h = __pyx_t_1;
- __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_stdout_f);
- __pyx_v_stdout_f = __pyx_t_3;
- __pyx_t_3 = 0;
- }
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2801);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2774
- * if catch_stdout:
- * stdout_h, stdout_f = tempfile.mkstemp()
- * stdout_save = Outs( sys.stdout.fileno() ) # <<<<<<<<<<<<<<
- * stdout_save.setfd( stdout_h )
- *
- */
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_4, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_stdout_save);
- __pyx_v_stdout_save = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2775
- * stdout_h, stdout_f = tempfile.mkstemp()
- * stdout_save = Outs( sys.stdout.fileno() )
- * stdout_save.setfd( stdout_h ) # <<<<<<<<<<<<<<
- *
- * # patch for `samtools view`
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(__pyx_v_stdout_h);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_h);
- __Pyx_GIVEREF(__pyx_v_stdout_h);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2780
- * # samtools `view` closes stdout, from which I can not
- * # recover. Thus redirect output to file with -o option.
- * if method == "view": # <<<<<<<<<<<<<<
- * if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
- * args = ( "-o", stdout_f ) + args
+/* "csamtools.pyx":2802
+ * """true is read is mapped to reverse strand"""
+ * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FMREVERSE
+ * else: self._delegate.core.flag &= ~BAM_FMREVERSE
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_method, ((PyObject *)__pyx_n_s__view), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2781
- * # recover. Thus redirect output to file with -o option.
- * if method == "view":
- * if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
- * args = ( "-o", stdout_f ) + args
- *
- */
- __pyx_t_5 = ((PySequence_Contains(__pyx_v_args, ((PyObject *)__pyx_kp_s_101)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_5) {
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_102));
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_kp_s_102));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_102));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
- }
- __pyx_L11:;
+static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2802);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2782
- * if method == "view":
- * if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
- * args = ( "-o", stdout_f ) + args # <<<<<<<<<<<<<<
- *
- *
+ /* "csamtools.pyx":2803
+ * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FMREVERSE # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FMREVERSE
+ * property is_read1:
*/
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_101));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_kp_s_101));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_101));
- __Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_stdout_f);
- __Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_4 = PyNumber_Add(__pyx_t_3, __pyx_v_args); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_args);
- __pyx_v_args = __pyx_t_4;
- __pyx_t_4 = 0;
- goto __pyx_L10;
- }
- __pyx_L10:;
- goto __pyx_L9;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 32);
+ goto __pyx_L3;
}
- __pyx_L9:;
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2789
- * cdef int i, n, retval
- *
- * n = len(args) # <<<<<<<<<<<<<<
- * # allocate two more for first (dummy) argument (contains command)
- * cargs = <char**>calloc( n+2, sizeof( char *) )
+ /* "csamtools.pyx":2804
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FMREVERSE
+ * else: self._delegate.core.flag &= ~BAM_FMREVERSE # <<<<<<<<<<<<<<
+ * property is_read1:
+ * """true if this is read1"""
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_args); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_n = __pyx_t_7;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~32));
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2791
- * n = len(args)
- * # allocate two more for first (dummy) argument (contains command)
- * cargs = <char**>calloc( n+2, sizeof( char *) ) # <<<<<<<<<<<<<<
- * cargs[0] = "samtools"
- * cargs[1] = method
- */
- __pyx_v_cargs = ((char **)calloc((__pyx_v_n + 2), (sizeof(char *))));
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2792
- * # allocate two more for first (dummy) argument (contains command)
- * cargs = <char**>calloc( n+2, sizeof( char *) )
- * cargs[0] = "samtools" # <<<<<<<<<<<<<<
- * cargs[1] = method
- * for i from 0 <= i < n: cargs[i+2] = args[i]
- */
- (__pyx_v_cargs[0]) = __pyx_k__samtools;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2793
- * cargs = <char**>calloc( n+2, sizeof( char *) )
- * cargs[0] = "samtools"
- * cargs[1] = method # <<<<<<<<<<<<<<
- * for i from 0 <= i < n: cargs[i+2] = args[i]
- * retval = pysam_dispatch(n+2, cargs)
- */
- __pyx_t_8 = PyBytes_AsString(__pyx_v_method); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_cargs[1]) = __pyx_t_8;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2794
- * cargs[0] = "samtools"
- * cargs[1] = method
- * for i from 0 <= i < n: cargs[i+2] = args[i] # <<<<<<<<<<<<<<
- * retval = pysam_dispatch(n+2, cargs)
- * free( cargs )
+/* "csamtools.pyx":2807
+ * property is_read1:
+ * """true if this is read1"""
+ * def __get__(self): return (self.flag & BAM_FREAD1) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREAD1
*/
- __pyx_t_9 = __pyx_v_n;
- for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_9; __pyx_v_i++) {
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_8 = PyBytes_AsString(__pyx_t_4); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- (__pyx_v_cargs[(__pyx_v_i + 2)]) = __pyx_t_8;
- }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2795
- * cargs[1] = method
- * for i from 0 <= i < n: cargs[i+2] = args[i]
- * retval = pysam_dispatch(n+2, cargs) # <<<<<<<<<<<<<<
- * free( cargs )
- *
- */
- __pyx_v_retval = pysam_dispatch((__pyx_v_n + 2), __pyx_v_cargs);
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2807);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_64); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2796
- * for i from 0 <= i < n: cargs[i+2] = args[i]
- * retval = pysam_dispatch(n+2, cargs)
- * free( cargs ) # <<<<<<<<<<<<<<
- *
- * # restore stdout/stderr. This will also flush, so
- */
- free(__pyx_v_cargs);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2800
- * # restore stdout/stderr. This will also flush, so
- * # needs to be before reading back the file contents
- * if catch_stdout: # <<<<<<<<<<<<<<
- * stdout_save.restore()
- * out_stdout = open( stdout_f, "r").readlines()
- */
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_5) {
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2801
- * # needs to be before reading back the file contents
- * if catch_stdout:
- * stdout_save.restore() # <<<<<<<<<<<<<<
- * out_stdout = open( stdout_f, "r").readlines()
- * os.remove( stdout_f )
+/* "csamtools.pyx":2808
+ * """true if this is read1"""
+ * def __get__(self): return (self.flag & BAM_FREAD1) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FREAD1
+ * else: self._delegate.core.flag &= ~BAM_FREAD1
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2802
- * if catch_stdout:
- * stdout_save.restore()
- * out_stdout = open( stdout_f, "r").readlines() # <<<<<<<<<<<<<<
- * os.remove( stdout_f )
- * else:
- */
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_f);
- __Pyx_GIVEREF(__pyx_v_stdout_f);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_4 = PyObject_Call(__pyx_builtin_open, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__readlines); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_v_out_stdout);
- __pyx_v_out_stdout = __pyx_t_4;
- __pyx_t_4 = 0;
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2808);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2803
- * stdout_save.restore()
- * out_stdout = open( stdout_f, "r").readlines()
- * os.remove( stdout_f ) # <<<<<<<<<<<<<<
- * else:
- * out_stdout = []
+ /* "csamtools.pyx":2809
+ * def __get__(self): return (self.flag & BAM_FREAD1) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREAD1 # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FREAD1
+ * property is_read2:
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__remove); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_stdout_f);
- __Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L14;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 64);
+ goto __pyx_L3;
}
/*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2805
- * os.remove( stdout_f )
- * else:
- * out_stdout = [] # <<<<<<<<<<<<<<
- *
- * if catch_stderr:
+ /* "csamtools.pyx":2810
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREAD1
+ * else: self._delegate.core.flag &= ~BAM_FREAD1 # <<<<<<<<<<<<<<
+ * property is_read2:
+ * """true if this is read2"""
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_v_out_stdout);
- __pyx_v_out_stdout = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~64));
}
- __pyx_L14:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2807
- * out_stdout = []
- *
- * if catch_stderr: # <<<<<<<<<<<<<<
- * stderr_save.restore()
- * out_stderr = open( stderr_f, "r").readlines()
- */
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stderr); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_5) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2808
- *
- * if catch_stderr:
- * stderr_save.restore() # <<<<<<<<<<<<<<
- * out_stderr = open( stderr_f, "r").readlines()
- * os.remove( stderr_f )
- */
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stderr_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2809
- * if catch_stderr:
- * stderr_save.restore()
- * out_stderr = open( stderr_f, "r").readlines() # <<<<<<<<<<<<<<
- * os.remove( stderr_f )
- * else:
- */
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_stderr_f);
- __Pyx_GIVEREF(__pyx_v_stderr_f);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_open, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_v_out_stderr);
- __pyx_v_out_stderr = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2810
- * stderr_save.restore()
- * out_stderr = open( stderr_f, "r").readlines()
- * os.remove( stderr_f ) # <<<<<<<<<<<<<<
- * else:
- * out_stderr = []
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_stderr_f);
- __Pyx_GIVEREF(__pyx_v_stderr_f);
- __pyx_t_3 = PyObject_Call(__pyx_t_4, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L15;
- }
- /*else*/ {
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2812
- * os.remove( stderr_f )
- * else:
- * out_stderr = [] # <<<<<<<<<<<<<<
- *
- * return retval, out_stderr, out_stdout
+/* "csamtools.pyx":2813
+ * property is_read2:
+ * """true if this is read2"""
+ * def __get__(self): return (self.flag & BAM_FREAD2) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREAD2
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_DECREF(__pyx_v_out_stderr);
- __pyx_v_out_stderr = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
- }
- __pyx_L15:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2814
- * out_stderr = []
- *
- * return retval, out_stderr, out_stdout # <<<<<<<<<<<<<<
- *
- * cdef class SNPCall:
- */
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2813);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __Pyx_INCREF(__pyx_v_out_stderr);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_out_stderr);
- __Pyx_GIVEREF(__pyx_v_out_stderr);
- __Pyx_INCREF(__pyx_v_out_stdout);
- PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_out_stdout);
- __Pyx_GIVEREF(__pyx_v_out_stdout);
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_128); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("csamtools._samtools_dispatch");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_stderr_h);
- __Pyx_DECREF(__pyx_v_stderr_f);
- __Pyx_DECREF(__pyx_v_stderr_save);
- __Pyx_DECREF(__pyx_v_stdout_h);
- __Pyx_DECREF(__pyx_v_stdout_f);
- __Pyx_DECREF(__pyx_v_stdout_save);
- __Pyx_DECREF(__pyx_v_out_stdout);
- __Pyx_DECREF(__pyx_v_out_stderr);
- __Pyx_DECREF(__pyx_v_args);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2829
- * property tid:
- * '''the chromosome ID as is defined in the header'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._tid
- *
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2814
+ * """true if this is read2"""
+ * def __get__(self): return (self.flag & BAM_FREAD2) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FREAD2
+ * else: self._delegate.core.flag &= ~BAM_FREAD2
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2829);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2814);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2830
- * '''the chromosome ID as is defined in the header'''
- * def __get__(self):
- * return self._tid # <<<<<<<<<<<<<<
- *
- * property pos:
+ /* "csamtools.pyx":2815
+ * def __get__(self): return (self.flag & BAM_FREAD2) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREAD2 # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FREAD2
+ * property is_secondary:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 128);
+ goto __pyx_L3;
+ }
+ /*else*/ {
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2816
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FREAD2
+ * else: self._delegate.core.flag &= ~BAM_FREAD2 # <<<<<<<<<<<<<<
+ * property is_secondary:
+ * """true if not primary alignment"""
+ */
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~128));
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.tid.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2834
- * property pos:
- * '''nucleotide position of SNP.'''
- * def __get__(self): return self._pos # <<<<<<<<<<<<<<
- *
- * property reference_base:
- */
-
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2834);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.pos.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2838
- * property reference_base:
- * '''reference base at pos. ``N`` if no reference sequence supplied.'''
- * def __get__(self): return PyString_FromStringAndSize( &self._reference_base, 1 ) # <<<<<<<<<<<<<<
- *
- * property genotype:
+/* "csamtools.pyx":2819
+ * property is_secondary:
+ * """true if not primary alignment"""
+ * def __get__(self): return (self.flag & BAM_FSECONDARY) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FSECONDARY
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2838);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2819);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyString_FromStringAndSize((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_256); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.reference_base.__get__");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2842
- * property genotype:
- * '''the genotype called.'''
- * def __get__(self): return PyString_FromStringAndSize( &self._genotype, 1 ) # <<<<<<<<<<<<<<
- *
- * property consensus_quality:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2820
+ * """true if not primary alignment"""
+ * def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FSECONDARY
+ * else: self._delegate.core.flag &= ~BAM_FSECONDARY
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2842);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyString_FromStringAndSize((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2820);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2821
+ * def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FSECONDARY # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FSECONDARY
+ * property is_qcfail:
+ */
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 256);
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2822
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FSECONDARY
+ * else: self._delegate.core.flag &= ~BAM_FSECONDARY # <<<<<<<<<<<<<<
+ * property is_qcfail:
+ * """true if QC failure"""
+ */
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~256));
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.genotype.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2846
- * property consensus_quality:
- * '''the genotype quality (Phred-scaled).'''
- * def __get__(self): return self._consensus_quality # <<<<<<<<<<<<<<
- *
- * property snp_quality:
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2825
+ * property is_qcfail:
+ * """true if QC failure"""
+ * def __get__(self): return (self.flag & BAM_FQCFAIL) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FQCFAIL
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2846);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2825);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_512); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.consensus_quality.__get__");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2850
- * property snp_quality:
- * '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
- * def __get__(self): return self._snp_quality # <<<<<<<<<<<<<<
- *
- * property mapping_quality:
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2826
+ * """true if QC failure"""
+ * def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FQCFAIL
+ * else: self._delegate.core.flag &= ~BAM_FQCFAIL
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2850);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2826);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2827
+ * def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FQCFAIL # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FQCFAIL
+ * property is_duplicate:
+ */
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 512);
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2828
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FQCFAIL
+ * else: self._delegate.core.flag &= ~BAM_FQCFAIL # <<<<<<<<<<<<<<
+ * property is_duplicate:
+ * """true if optical or PCR duplicate"""
+ */
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~512));
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.snp_quality.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2854
- * property mapping_quality:
- * '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
- * def __get__(self): return self._rms_mapping_quality # <<<<<<<<<<<<<<
- *
- * property coverage:
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2831
+ * property is_duplicate:
+ * """true if optical or PCR duplicate"""
+ * def __get__(self): return (self.flag & BAM_FDUP) != 0 # <<<<<<<<<<<<<<
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FDUP
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2854);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2831);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_1024); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.mapping_quality.__get__");
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2858
- * property coverage:
- * '''coverage or read depth - the number of reads involved in the call.'''
- * def __get__(self): return self._coverage # <<<<<<<<<<<<<<
- *
- * def __str__(self):
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2832
+ * """true if optical or PCR duplicate"""
+ * def __get__(self): return (self.flag & BAM_FDUP) != 0
+ * def __set__(self,val): # <<<<<<<<<<<<<<
+ * if val: self._delegate.core.flag |= BAM_FDUP
+ * else: self._delegate.core.flag &= ~BAM_FDUP
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2858);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2832);
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2833
+ * def __get__(self): return (self.flag & BAM_FDUP) != 0
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FDUP # <<<<<<<<<<<<<<
+ * else: self._delegate.core.flag &= ~BAM_FDUP
+ * property positions:
+ */
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1024);
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":2834
+ * def __set__(self,val):
+ * if val: self._delegate.core.flag |= BAM_FDUP
+ * else: self._delegate.core.flag &= ~BAM_FDUP # <<<<<<<<<<<<<<
+ * property positions:
+ * """a list of reference positions that this read aligns to."""
+ */
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1024));
+ }
+ __pyx_L3:;
+
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.coverage.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2860
- * def __get__(self): return self._coverage
- *
- * def __str__(self): # <<<<<<<<<<<<<<
- *
- * return "\t".join( map(str, (
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9positions___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2837
+ * property positions:
+ * """a list of reference positions that this read aligns to."""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef uint32_t k, i, pos
+ * cdef int op
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_i;
+ uint32_t __pyx_v_pos;
+ int __pyx_v_op;
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_result = NULL;
+ PyObject *__pyx_v_l = NULL;
PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ uint32_t __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
+ uint32_t __pyx_t_5;
+ int __pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 2860);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2837);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2862
- * def __str__(self):
+ /* "csamtools.pyx":2843
+ * cdef bam1_t * src
+ *
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.core.n_cigar == 0: return []
*
- * return "\t".join( map(str, ( # <<<<<<<<<<<<<<
- * self.tid,
- * self.pos,
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2863
+ /* "csamtools.pyx":2844
*
- * return "\t".join( map(str, (
- * self.tid, # <<<<<<<<<<<<<<
- * self.pos,
- * self.reference_base,
+ * src = self._delegate
+ * if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
+ *
+ * result = []
+ */
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":2846
+ * if src.core.n_cigar == 0: return []
+ *
+ * result = [] # <<<<<<<<<<<<<<
+ * pos = src.core.pos
+ * cigar_p = bam1_cigar(src)
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2864
- * return "\t".join( map(str, (
- * self.tid,
- * self.pos, # <<<<<<<<<<<<<<
- * self.reference_base,
- * self.genotype,
+ /* "csamtools.pyx":2847
+ *
+ * result = []
+ * pos = src.core.pos # <<<<<<<<<<<<<<
+ * cigar_p = bam1_cigar(src)
+ *
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_pos = __pyx_v_src->core.pos;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2865
- * self.tid,
- * self.pos,
- * self.reference_base, # <<<<<<<<<<<<<<
- * self.genotype,
- * self.consensus_quality,
+ /* "csamtools.pyx":2848
+ * result = []
+ * pos = src.core.pos
+ * cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
+ *
+ * for k from 0 <= k < src.core.n_cigar:
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2866
- * self.pos,
- * self.reference_base,
- * self.genotype, # <<<<<<<<<<<<<<
- * self.consensus_quality,
- * self.snp_quality,
+ /* "csamtools.pyx":2850
+ * cigar_p = bam1_cigar(src)
+ *
+ * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2867
- * self.reference_base,
- * self.genotype,
- * self.consensus_quality, # <<<<<<<<<<<<<<
- * self.snp_quality,
- * self.mapping_quality,
+ /* "csamtools.pyx":2851
+ *
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * if op == BAM_CMATCH:
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2868
- * self.genotype,
- * self.consensus_quality,
- * self.snp_quality, # <<<<<<<<<<<<<<
- * self.mapping_quality,
- * self.coverage ) ) )
+ /* "csamtools.pyx":2852
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
+ * if op == BAM_CMATCH:
+ * for i from pos <= i < pos + l:
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_l);
+ __pyx_v_l = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2869
- * self.consensus_quality,
- * self.snp_quality,
- * self.mapping_quality, # <<<<<<<<<<<<<<
- * self.coverage ) ) )
+ /* "csamtools.pyx":2853
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * if op == BAM_CMATCH: # <<<<<<<<<<<<<<
+ * for i from pos <= i < pos + l:
+ * result.append( i )
+ */
+ __pyx_t_1 = (__pyx_v_op == 0);
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":2854
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ * if op == BAM_CMATCH:
+ * for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
+ * result.append( i )
*
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2870
- * self.snp_quality,
- * self.mapping_quality,
- * self.coverage ) ) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2855
+ * if op == BAM_CMATCH:
+ * for i from pos <= i < pos + l:
+ * result.append( i ) # <<<<<<<<<<<<<<
+ *
+ * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ */
+ __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = PyList_Append(__pyx_v_result, __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ }
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+
+ /* "csamtools.pyx":2857
+ * result.append( i )
*
+ * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
+ * pos += l
*
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_10, 4, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_10, 5, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_10, 6, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_10, 7, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_2 = 0;
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_7 = 0;
- __pyx_t_8 = 0;
- __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_map, __pyx_t_9, NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_1, __pyx_t_9, NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_r = __pyx_t_10;
- __pyx_t_10 = 0;
- goto __pyx_L0;
+ switch (__pyx_v_op) {
+ case 0:
+ case 2:
+ case 3:
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
+ /* "csamtools.pyx":2858
+ *
+ * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ * pos += l # <<<<<<<<<<<<<<
+ *
+ * return result
+ */
+ __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_2); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_pos = __pyx_t_5;
+ break;
+ }
+ }
+
+ /* "csamtools.pyx":2860
+ * pos += l
+ *
+ * return result # <<<<<<<<<<<<<<
+ *
+ * property aligned_pairs:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_result));
+ __pyx_r = ((PyObject *)__pyx_v_result);
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.SNPCall.__str__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.positions.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_result);
+ __Pyx_XDECREF(__pyx_v_l);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2891
- * cdef IteratorColumn iter
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * IteratorColumn iterator_column,
- * **kwargs ):
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":2867
+ * Unaligned position are marked by None.
+ * """
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef uint32_t k, i, pos, qpos
+ * cdef int op
*/
-static int __pyx_pf_9csamtools_13SNPCallerBase___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_13SNPCallerBase___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_iterator_column = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_i;
+ uint32_t __pyx_v_pos;
+ uint32_t __pyx_v_qpos;
+ int __pyx_v_op;
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_result = NULL;
+ PyObject *__pyx_v_l = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- float __pyx_t_4;
- int __pyx_t_5;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__iterator_column,0};
+ uint32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ uint32_t __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ int __pyx_t_7;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 2891);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__iterator_column);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2891; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)PyTuple_GET_ITEM(__pyx_args, 0));
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2891; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.SNPCallerBase.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_iterator_column), __pyx_ptype_9csamtools_IteratorColumn, 1, "iterator_column", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2867);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2895
- * **kwargs ):
+ /* "csamtools.pyx":2873
+ * cdef bam1_t * src
*
- * self.iter = iterator_column # <<<<<<<<<<<<<<
- * self.c = bam_maqcns_init()
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.core.n_cigar == 0: return []
*
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_iterator_column));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_iterator_column));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->iter);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->iter));
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->iter = __pyx_v_iterator_column;
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2896
+ /* "csamtools.pyx":2874
*
- * self.iter = iterator_column
- * self.c = bam_maqcns_init() # <<<<<<<<<<<<<<
+ * src = self._delegate
+ * if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
*
- * # set the default parameterization according to
+ * result = []
*/
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c = bam_maqcns_init();
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2902
+ /* "csamtools.pyx":2876
+ * if src.core.n_cigar == 0: return []
*
- * # new default mode for samtools >0.1.10
- * self.c.errmod = kwargs.get( "errmod", BAM_ERRMOD_MAQ2 ) # <<<<<<<<<<<<<<
- *
- * self.c.min_baseQ = kwargs.get( "min_baseQ", 13 )
+ * result = [] # <<<<<<<<<<<<<<
+ * pos = src.core.pos
+ * qpos = 0
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyInt_FromLong(BAM_ERRMOD_MAQ2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__errmod), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->errmod = __pyx_t_3;
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2904
- * self.c.errmod = kwargs.get( "errmod", BAM_ERRMOD_MAQ2 )
+ /* "csamtools.pyx":2877
*
- * self.c.min_baseQ = kwargs.get( "min_baseQ", 13 ) # <<<<<<<<<<<<<<
- * # self.c.capQ_thres = kwargs.get( "capQ_threshold", 60 )
- * self.c.n_hap = kwargs.get( "n_haplotypes", 2 )
+ * result = []
+ * pos = src.core.pos # <<<<<<<<<<<<<<
+ * qpos = 0
+ * cigar_p = bam1_cigar(src)
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__min_baseQ), __pyx_int_13); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->min_baseQ = __pyx_t_3;
+ __pyx_v_pos = __pyx_v_src->core.pos;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2906
- * self.c.min_baseQ = kwargs.get( "min_baseQ", 13 )
- * # self.c.capQ_thres = kwargs.get( "capQ_threshold", 60 )
- * self.c.n_hap = kwargs.get( "n_haplotypes", 2 ) # <<<<<<<<<<<<<<
- * self.c.het_rate = kwargs.get( "het_rate", 0.001 )
- * self.c.theta = kwargs.get( "theta", 0.83 )
+ /* "csamtools.pyx":2878
+ * result = []
+ * pos = src.core.pos
+ * qpos = 0 # <<<<<<<<<<<<<<
+ * cigar_p = bam1_cigar(src)
+ *
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__n_haplotypes), __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->n_hap = __pyx_t_3;
+ __pyx_v_qpos = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2907
- * # self.c.capQ_thres = kwargs.get( "capQ_threshold", 60 )
- * self.c.n_hap = kwargs.get( "n_haplotypes", 2 )
- * self.c.het_rate = kwargs.get( "het_rate", 0.001 ) # <<<<<<<<<<<<<<
- * self.c.theta = kwargs.get( "theta", 0.83 )
+ /* "csamtools.pyx":2879
+ * pos = src.core.pos
+ * qpos = 0
+ * cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
*
+ * for k from 0 <= k < src.core.n_cigar:
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyFloat_FromDouble(0.001); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__het_rate), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __pyx_PyFloat_AsDouble(__pyx_t_1); if (unlikely((__pyx_t_4 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->het_rate = __pyx_t_4;
+ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2908
- * self.c.n_hap = kwargs.get( "n_haplotypes", 2 )
- * self.c.het_rate = kwargs.get( "het_rate", 0.001 )
- * self.c.theta = kwargs.get( "theta", 0.83 ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2881
+ * cigar_p = bam1_cigar(src)
*
- * if self.c.errmod != BAM_ERRMOD_MAQ2:
+ * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyFloat_FromDouble(0.83); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__theta), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __pyx_PyFloat_AsDouble(__pyx_t_2); if (unlikely((__pyx_t_4 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->theta = __pyx_t_4;
+ __pyx_t_3 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2910
- * self.c.theta = kwargs.get( "theta", 0.83 )
+ /* "csamtools.pyx":2882
*
- * if self.c.errmod != BAM_ERRMOD_MAQ2: # <<<<<<<<<<<<<<
- * self.c.theta += 0.02
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
*/
- __pyx_t_5 = (((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->errmod != BAM_ERRMOD_MAQ2);
- if (__pyx_t_5) {
+ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2911
+ /* "csamtools.pyx":2883
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
*
- * if self.c.errmod != BAM_ERRMOD_MAQ2:
- * self.c.theta += 0.02 # <<<<<<<<<<<<<<
- *
- * # call prepare AFTER setting parameters
+ * if op == BAM_CMATCH:
*/
- ((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c->theta += 0.02;
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_l);
+ __pyx_v_l = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2914
- *
- * # call prepare AFTER setting parameters
- * bam_maqcns_prepare( self.c ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2896
+ * qpos += 1
*
- * def __dealloc__(self):
+ * elif op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
+ * for i from pos <= i < pos + l:
+ * result.append( (None, i) )
*/
- bam_maqcns_prepare(((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c);
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.SNPCallerBase.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ switch (__pyx_v_op) {
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2916
- * bam_maqcns_prepare( self.c )
- *
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * bam_maqcns_destroy( self.c )
+ /* "csamtools.pyx":2885
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
+ * if op == BAM_CMATCH: # <<<<<<<<<<<<<<
+ * for i from pos <= i < pos + l:
+ * result.append( (qpos, i) )
*/
+ case 0:
-static void __pyx_pf_9csamtools_13SNPCallerBase___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_13SNPCallerBase___dealloc__(PyObject *__pyx_v_self) {
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 2916);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2917
- *
- * def __dealloc__(self):
- * bam_maqcns_destroy( self.c ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2886
*
- * cdef __dump( self, glf1_t * g, uint32_t cns, int rb ):
+ * if op == BAM_CMATCH:
+ * for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
+ * result.append( (qpos, i) )
+ * qpos += 1
*/
- bam_maqcns_destroy(((struct __pyx_obj_9csamtools_SNPCallerBase *)__pyx_v_self)->c);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
+ /* "csamtools.pyx":2887
+ * if op == BAM_CMATCH:
+ * for i from pos <= i < pos + l:
+ * result.append( (qpos, i) ) # <<<<<<<<<<<<<<
+ * qpos += 1
+ * pos += l
+ */
+ __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_4 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2919
- * bam_maqcns_destroy( self.c )
- *
- * cdef __dump( self, glf1_t * g, uint32_t cns, int rb ): # <<<<<<<<<<<<<<
- * '''debugging output.'''
+ /* "csamtools.pyx":2888
+ * for i from pos <= i < pos + l:
+ * result.append( (qpos, i) )
+ * qpos += 1 # <<<<<<<<<<<<<<
+ * pos += l
*
*/
+ __pyx_v_qpos = (__pyx_v_qpos + 1);
+ }
-static PyObject *__pyx_f_9csamtools_13SNPCallerBase___dump(struct __pyx_obj_9csamtools_SNPCallerBase *__pyx_v_self, glf1_t *__pyx_v_g, uint32_t __pyx_v_cns, int __pyx_v_rb) {
- int __pyx_v_x;
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- PyObject *__pyx_t_12 = NULL;
- PyObject *__pyx_t_13 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dump");
- __Pyx_TraceCall("__dump", __pyx_f[0], 2919);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2922
- * '''debugging output.'''
+ /* "csamtools.pyx":2889
+ * result.append( (qpos, i) )
+ * qpos += 1
+ * pos += l # <<<<<<<<<<<<<<
*
- * pysam_dump_glf( g, self.c ); # <<<<<<<<<<<<<<
- * print ""
- * for x in range(self.iter.n_plp):
+ * elif op == BAM_CINS:
*/
- pysam_dump_glf(__pyx_v_g, __pyx_v_self->c);
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_2); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_pos = __pyx_t_5;
+ break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2923
+ /* "csamtools.pyx":2891
+ * pos += l
*
- * pysam_dump_glf( g, self.c );
- * print "" # <<<<<<<<<<<<<<
- * for x in range(self.iter.n_plp):
- * print "--> read %i %s %i" % (x,
+ * elif op == BAM_CINS: # <<<<<<<<<<<<<<
+ * for i from pos <= i < pos + l:
+ * result.append( (qpos, None) )
*/
- if (__Pyx_PrintOne(0, ((PyObject *)__pyx_kp_s_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ case 1:
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2924
- * pysam_dump_glf( g, self.c );
- * print ""
- * for x in range(self.iter.n_plp): # <<<<<<<<<<<<<<
- * print "--> read %i %s %i" % (x,
- * bam1_qname(self.iter.plp[x].b),
+ /* "csamtools.pyx":2892
+ *
+ * elif op == BAM_CINS:
+ * for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
+ * result.append( (qpos, None) )
+ * qpos += 1
*/
- __pyx_t_1 = __pyx_v_self->iter->n_plp;
- for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
- __pyx_v_x = __pyx_t_2;
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2925
- * print ""
- * for x in range(self.iter.n_plp):
- * print "--> read %i %s %i" % (x, # <<<<<<<<<<<<<<
- * bam1_qname(self.iter.plp[x].b),
- * self.iter.plp[x].qpos,
+ /* "csamtools.pyx":2893
+ * elif op == BAM_CINS:
+ * for i from pos <= i < pos + l:
+ * result.append( (qpos, None) ) # <<<<<<<<<<<<<<
+ * qpos += 1
+ *
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_v_x); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __pyx_t_6 = 0;
+ __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2926
- * for x in range(self.iter.n_plp):
- * print "--> read %i %s %i" % (x,
- * bam1_qname(self.iter.plp[x].b), # <<<<<<<<<<<<<<
- * self.iter.plp[x].qpos,
- * )
+ /* "csamtools.pyx":2894
+ * for i from pos <= i < pos + l:
+ * result.append( (qpos, None) )
+ * qpos += 1 # <<<<<<<<<<<<<<
+ *
+ * elif op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
- __pyx_t_4 = PyBytes_FromString(bam1_qname((__pyx_v_self->iter->plp[__pyx_v_x]).b)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_v_qpos = (__pyx_v_qpos + 1);
+ }
+ break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2927
- * print "--> read %i %s %i" % (x,
- * bam1_qname(self.iter.plp[x].b),
- * self.iter.plp[x].qpos, # <<<<<<<<<<<<<<
- * )
+ /* "csamtools.pyx":2896
+ * qpos += 1
*
+ * elif op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
+ * for i from pos <= i < pos + l:
+ * result.append( (None, i) )
*/
- __pyx_t_5 = __Pyx_PyInt_to_py_int32_t((__pyx_v_self->iter->plp[__pyx_v_x]).qpos); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_3 = 0;
- __pyx_t_4 = 0;
- __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_104), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__Pyx_PrintOne(0, ((PyObject *)__pyx_t_5)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- }
+ case 2:
+ case 3:
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2931
+ /* "csamtools.pyx":2897
*
- * print "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i" \
- * % (self.iter.pos, # <<<<<<<<<<<<<<
- * cns,
- * self.c.q_r,
+ * elif op == BAM_CDEL or op == BAM_CREF_SKIP:
+ * for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
+ * result.append( (None, i) )
+ * pos += l
*/
- __pyx_t_5 = PyInt_FromLong(__pyx_v_self->iter->pos); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2932
- * print "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i" \
- * % (self.iter.pos,
- * cns, # <<<<<<<<<<<<<<
- * self.c.q_r,
- * self.iter.n_plp,
+ /* "csamtools.pyx":2898
+ * elif op == BAM_CDEL or op == BAM_CREF_SKIP:
+ * for i from pos <= i < pos + l:
+ * result.append( (None, i) ) # <<<<<<<<<<<<<<
+ * pos += l
+ *
*/
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_cns); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2933
- * % (self.iter.pos,
- * cns,
- * self.c.q_r, # <<<<<<<<<<<<<<
- * self.iter.n_plp,
- * self.iter.n_plp,
+ /* "csamtools.pyx":2899
+ * for i from pos <= i < pos + l:
+ * result.append( (None, i) )
+ * pos += l # <<<<<<<<<<<<<<
+ *
+ * return result
*/
- __pyx_t_4 = PyFloat_FromDouble(__pyx_v_self->c->q_r); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_InPlaceAdd(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_v_pos = __pyx_t_5;
+ break;
+ }
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2934
- * cns,
- * self.c.q_r,
- * self.iter.n_plp, # <<<<<<<<<<<<<<
- * self.iter.n_plp,
- * rb,
+ /* "csamtools.pyx":2901
+ * pos += l
+ *
+ * return result # <<<<<<<<<<<<<<
+ *
+ *
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_v_self->iter->n_plp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_result));
+ __pyx_r = ((PyObject *)__pyx_v_result);
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2935
- * self.c.q_r,
- * self.iter.n_plp,
- * self.iter.n_plp, # <<<<<<<<<<<<<<
- * rb,
- * cns >> 8 & 0xff,
- */
- __pyx_t_7 = PyInt_FromLong(__pyx_v_self->iter->n_plp); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2935; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_AddTraceback("csamtools.AlignedRead.aligned_pairs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_result);
+ __Pyx_XDECREF(__pyx_v_l);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2936
- * self.iter.n_plp,
- * self.iter.n_plp,
- * rb, # <<<<<<<<<<<<<<
- * cns >> 8 & 0xff,
- * cns >> 16 & 0xff,
- */
- __pyx_t_8 = PyInt_FromLong(__pyx_v_rb); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2937
- * self.iter.n_plp,
- * rb,
- * cns >> 8 & 0xff, # <<<<<<<<<<<<<<
- * cns >> 16 & 0xff,
- * cns & 0xff,
- */
- __pyx_t_9 = PyInt_FromLong(((__pyx_v_cns >> 8) & 0xff)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2938
- * rb,
- * cns >> 8 & 0xff,
- * cns >> 16 & 0xff, # <<<<<<<<<<<<<<
- * cns & 0xff,
- * cns >> 28,
- */
- __pyx_t_10 = PyInt_FromLong(((__pyx_v_cns >> 16) & 0xff)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2939
- * cns >> 8 & 0xff,
- * cns >> 16 & 0xff,
- * cns & 0xff, # <<<<<<<<<<<<<<
- * cns >> 28,
- * )
- */
- __pyx_t_11 = PyInt_FromLong((__pyx_v_cns & 0xff)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2940
- * cns >> 16 & 0xff,
- * cns & 0xff,
- * cns >> 28, # <<<<<<<<<<<<<<
- * )
- *
- */
- __pyx_t_12 = PyInt_FromLong((__pyx_v_cns >> 28)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __pyx_t_13 = PyTuple_New(10); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_13, 2, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_13, 3, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_13, 4, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_13, 5, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_13, 6, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_13, 7, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_13, 8, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
- PyTuple_SET_ITEM(__pyx_t_13, 9, __pyx_t_12);
- __Pyx_GIVEREF(__pyx_t_12);
- __pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_4 = 0;
- __pyx_t_3 = 0;
- __pyx_t_7 = 0;
- __pyx_t_8 = 0;
- __pyx_t_9 = 0;
- __pyx_t_10 = 0;
- __pyx_t_11 = 0;
- __pyx_t_12 = 0;
- __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_105), __pyx_t_13); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_12));
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- if (__Pyx_PrintOne(0, ((PyObject *)__pyx_t_12)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2943
- * )
- *
- * printf("-------------------------------------\n"); # <<<<<<<<<<<<<<
- * sys.stdout.flush()
- *
- */
- printf(__pyx_k_106);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2944
- *
- * printf("-------------------------------------\n");
- * sys.stdout.flush() # <<<<<<<<<<<<<<
- *
- * cdef class IteratorSNPCalls( SNPCallerBase ):
- */
- __pyx_t_12 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __pyx_t_13 = PyObject_GetAttr(__pyx_t_12, __pyx_n_s__stdout); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_12 = PyObject_GetAttr(__pyx_t_13, __pyx_n_s__flush); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_13 = PyObject_Call(__pyx_t_12, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_XDECREF(__pyx_t_12);
- __Pyx_XDECREF(__pyx_t_13);
- __Pyx_AddTraceback("csamtools.SNPCallerBase.__dump");
- __pyx_r = 0;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2960
- * """
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * IteratorColumn iterator_column,
- * **kwargs ):
- */
-
-static int __pyx_pf_9csamtools_16IteratorSNPCalls___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_16IteratorSNPCalls___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_iterator_column = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__iterator_column,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 2960);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__iterator_column);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2960; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)PyTuple_GET_ITEM(__pyx_args, 0));
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_10overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ uint32_t __pyx_v_start;
+ uint32_t __pyx_v_end;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("overlap (wrapper)", 0);
+ {
+ PyObject* values[2] = {0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ }
+ __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(values[0]); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(values[1]); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2960; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IteratorSNPCalls.__cinit__");
+ __Pyx_AddTraceback("csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
- return -1;
+ return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_iterator_column), __pyx_ptype_9csamtools_IteratorColumn, 1, "iterator_column", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2964
- * **kwargs ):
- *
- * assert self.iter.hasReference(), "IteratorSNPCalls requires an pileup iterator with reference sequence" # <<<<<<<<<<<<<<
- *
- * def __iter__(self):
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter), __pyx_n_s__hasReference); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(!__pyx_t_3)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_107));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorSNPCalls.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10overlap(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), __pyx_v_start, __pyx_v_end);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2966
- * assert self.iter.hasReference(), "IteratorSNPCalls requires an pileup iterator with reference sequence"
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
- *
- */
-
-static PyObject *__pyx_pf_9csamtools_16IteratorSNPCalls___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_16IteratorSNPCalls___iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 2966);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2967
+/* "csamtools.pyx":2904
*
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
- *
- * def __next__(self):
- */
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2969
- * return self
*
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
- * """
+ * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
+ * """return number of aligned bases of read overlapping the interval *start* and *end*
+ * on the reference sequence.
*/
-static PyObject *__pyx_pf_9csamtools_16IteratorSNPCalls___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_16IteratorSNPCalls___next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__;
-static PyObject *__pyx_pf_9csamtools_16IteratorSNPCalls___next__(PyObject *__pyx_v_self) {
- char *__pyx_v_seq;
- int __pyx_v_seq_len;
- int __pyx_v_rb;
- uint32_t __pyx_v_cns;
- glf1_t *__pyx_v_g;
- struct __pyx_obj_9csamtools_SNPCall *__pyx_v_call;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_pos;
+ uint32_t __pyx_v_overlap;
+ int __pyx_v_op;
+ int __pyx_v_o;
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_l = NULL;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ uint32_t __pyx_t_2;
PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
+ uint32_t __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ uint32_t __pyx_t_8;
+ uint32_t __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 2969);
- __pyx_v_call = ((struct __pyx_obj_9csamtools_SNPCall *)Py_None); __Pyx_INCREF(Py_None);
+ __Pyx_RefNannySetupContext("overlap", 0);
+ __Pyx_TraceCall("overlap", __pyx_f[0], 2904);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2974
+ /* "csamtools.pyx":2913
+ * cdef bam1_t * src
*
- * # the following code was adapted from bam_plcmd.c:pileup_func()
- * self.iter.cnext() # <<<<<<<<<<<<<<
+ * overlap = 0 # <<<<<<<<<<<<<<
*
- * if self.iter.n_plp < 0:
+ * src = self._delegate
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter);
+ __pyx_v_overlap = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2976
- * self.iter.cnext()
- *
- * if self.iter.n_plp < 0: # <<<<<<<<<<<<<<
- * raise ValueError("error during iteration" )
+ /* "csamtools.pyx":2915
+ * overlap = 0
*
+ * src = self._delegate # <<<<<<<<<<<<<<
+ * if src.core.n_cigar == 0: return 0
+ * pos = src.core.pos
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->n_plp < 0);
- if (__pyx_t_1) {
+ __pyx_v_src = __pyx_v_self->_delegate;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2977
+ /* "csamtools.pyx":2916
*
- * if self.iter.n_plp < 0:
- * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
- *
- * if self.iter.plp == NULL:
+ * src = self._delegate
+ * if src.core.n_cigar == 0: return 0 # <<<<<<<<<<<<<<
+ * pos = src.core.pos
+ * o = 0
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_59));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_59));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_59));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(__pyx_int_0);
+ __pyx_r = __pyx_int_0;
+ goto __pyx_L0;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2979
- * raise ValueError("error during iteration" )
- *
- * if self.iter.plp == NULL: # <<<<<<<<<<<<<<
- * raise StopIteration
+ /* "csamtools.pyx":2917
+ * src = self._delegate
+ * if src.core.n_cigar == 0: return 0
+ * pos = src.core.pos # <<<<<<<<<<<<<<
+ * o = 0
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->plp == NULL);
- if (__pyx_t_1) {
+ __pyx_v_pos = __pyx_v_src->core.pos;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2980
- *
- * if self.iter.plp == NULL:
- * raise StopIteration # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2918
+ * if src.core.n_cigar == 0: return 0
+ * pos = src.core.pos
+ * o = 0 # <<<<<<<<<<<<<<
*
- * cdef char * seq = self.iter.getSequence()
+ * cigar_p = bam1_cigar(src)
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_v_o = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2982
- * raise StopIteration
- *
- * cdef char * seq = self.iter.getSequence() # <<<<<<<<<<<<<<
- * cdef int seq_len = self.iter.seq_len
+ /* "csamtools.pyx":2920
+ * o = 0
*
+ * cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
*/
- __pyx_v_seq = ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->getSequence(((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter);
+ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2983
- *
- * cdef char * seq = self.iter.getSequence()
- * cdef int seq_len = self.iter.seq_len # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2921
*
- * assert seq != NULL
+ * cigar_p = bam1_cigar(src)
+ * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter), __pyx_n_s__seq_len); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_seq_len = __pyx_t_4;
+ __pyx_t_2 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_2; __pyx_v_k++) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2985
- * cdef int seq_len = self.iter.seq_len
- *
- * assert seq != NULL # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2922
+ * cigar_p = bam1_cigar(src)
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
- * # reference base
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_seq != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2988
- *
- * # reference base
- * if self.iter.pos >= seq_len: # <<<<<<<<<<<<<<
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
+ /* "csamtools.pyx":2923
+ * for k from 0 <= k < src.core.n_cigar:
+ * op = cigar_p[k] & BAM_CIGAR_MASK
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
*
+ * if op == BAM_CMATCH:
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->pos >= __pyx_v_seq_len);
- if (__pyx_t_1) {
+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_v_l);
+ __pyx_v_l = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2989
- * # reference base
- * if self.iter.pos >= seq_len:
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2925
+ * l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
- * cdef int rb = seq[self.iter.pos]
+ * if op == BAM_CMATCH: # <<<<<<<<<<<<<<
+ * o = min( pos + l, end) - max( pos, start )
+ * if o > 0: overlap += o
*/
- __pyx_t_3 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_seq_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_3 = 0;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
- }
- __pyx_L7:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2991
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
- *
- * cdef int rb = seq[self.iter.pos] # <<<<<<<<<<<<<<
- * cdef uint32_t cns
- * cdef glf1_t * g
- */
- __pyx_v_rb = (__pyx_v_seq[((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->pos]);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2998
- * self.iter.plp,
- * bam_nt16_table[rb],
- * self.c ) # <<<<<<<<<<<<<<
- *
- * if pysam_glf_depth( g ) == 0:
- */
- __pyx_v_g = bam_maqcns_glfgen(((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->n_plp, ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->plp, (bam_nt16_table[__pyx_v_rb]), ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.c);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3000
- * self.c )
- *
- * if pysam_glf_depth( g ) == 0: # <<<<<<<<<<<<<<
- * cns = 0xfu << 28 | 0xf << 24
- * else:
- */
- __pyx_t_1 = (pysam_glf_depth(__pyx_v_g) == 0);
- if (__pyx_t_1) {
+ __pyx_t_1 = (__pyx_v_op == 0);
+ if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3001
+ /* "csamtools.pyx":2926
*
- * if pysam_glf_depth( g ) == 0:
- * cns = 0xfu << 28 | 0xf << 24 # <<<<<<<<<<<<<<
- * else:
- * cns = glf2cns(g, <int>(self.c.q_r + .499))
- */
- __pyx_v_cns = 4278190080U;
- goto __pyx_L8;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3003
- * cns = 0xfu << 28 | 0xf << 24
- * else:
- * cns = glf2cns(g, <int>(self.c.q_r + .499)) # <<<<<<<<<<<<<<
+ * if op == BAM_CMATCH:
+ * o = min( pos + l, end) - max( pos, start ) # <<<<<<<<<<<<<<
+ * if o > 0: overlap += o
*
- * free(g)
*/
- __pyx_v_cns = glf2cns(__pyx_v_g, ((int)(((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.c->q_r + .499)));
- }
- __pyx_L8:;
+ __pyx_t_4 = __pyx_v_end;
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_1) {
+ __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_3 = __pyx_t_7;
+ __pyx_t_7 = 0;
+ } else {
+ __Pyx_INCREF(__pyx_t_5);
+ __pyx_t_3 = __pyx_t_5;
+ }
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __pyx_v_start;
+ __pyx_t_8 = __pyx_v_pos;
+ if ((__pyx_t_4 > __pyx_t_8)) {
+ __pyx_t_9 = __pyx_t_4;
+ } else {
+ __pyx_t_9 = __pyx_t_8;
+ }
+ __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyNumber_Subtract(__pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_v_o = __pyx_t_10;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3005
- * cns = glf2cns(g, <int>(self.c.q_r + .499))
- *
- * free(g) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":2927
+ * if op == BAM_CMATCH:
+ * o = min( pos + l, end) - max( pos, start )
+ * if o > 0: overlap += o # <<<<<<<<<<<<<<
*
- * cdef SNPCall call
+ * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
- free(__pyx_v_g);
+ __pyx_t_1 = (__pyx_v_o > 0);
+ if (__pyx_t_1) {
+ __pyx_v_overlap = (__pyx_v_overlap + __pyx_v_o);
+ goto __pyx_L7;
+ }
+ __pyx_L7:;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3009
- * cdef SNPCall call
+ /* "csamtools.pyx":2929
+ * if o > 0: overlap += o
*
- * call = SNPCall() # <<<<<<<<<<<<<<
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos
- */
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_SNPCall)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_v_call));
- __pyx_v_call = ((struct __pyx_obj_9csamtools_SNPCall *)__pyx_t_2);
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3010
+ * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
+ * pos += l
*
- * call = SNPCall()
- * call._tid = self.iter.tid # <<<<<<<<<<<<<<
- * call._pos = self.iter.pos
- * call._reference_base = rb
- */
- __pyx_v_call->_tid = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->tid;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3011
- * call = SNPCall()
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos # <<<<<<<<<<<<<<
- * call._reference_base = rb
- * call._genotype = bam_nt16_rev_table[cns>>28]
- */
- __pyx_v_call->_pos = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->pos;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3012
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos
- * call._reference_base = rb # <<<<<<<<<<<<<<
- * call._genotype = bam_nt16_rev_table[cns>>28]
- * call._consensus_quality = cns >> 8 & 0xff
- */
- __pyx_v_call->_reference_base = __pyx_v_rb;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3013
- * call._pos = self.iter.pos
- * call._reference_base = rb
- * call._genotype = bam_nt16_rev_table[cns>>28] # <<<<<<<<<<<<<<
- * call._consensus_quality = cns >> 8 & 0xff
- * call._snp_quality = cns & 0xff
- */
- __pyx_v_call->_genotype = (__pyx_v_9csamtools_bam_nt16_rev_table[(__pyx_v_cns >> 28)]);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3014
- * call._reference_base = rb
- * call._genotype = bam_nt16_rev_table[cns>>28]
- * call._consensus_quality = cns >> 8 & 0xff # <<<<<<<<<<<<<<
- * call._snp_quality = cns & 0xff
- * call._rms_mapping_quality = cns >> 16&0xff
- */
- __pyx_v_call->_consensus_quality = ((__pyx_v_cns >> 8) & 0xff);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3015
- * call._genotype = bam_nt16_rev_table[cns>>28]
- * call._consensus_quality = cns >> 8 & 0xff
- * call._snp_quality = cns & 0xff # <<<<<<<<<<<<<<
- * call._rms_mapping_quality = cns >> 16&0xff
- * call._coverage = self.iter.n_plp
*/
- __pyx_v_call->_snp_quality = (__pyx_v_cns & 0xff);
+ switch (__pyx_v_op) {
+ case 0:
+ case 2:
+ case 3:
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3016
- * call._consensus_quality = cns >> 8 & 0xff
- * call._snp_quality = cns & 0xff
- * call._rms_mapping_quality = cns >> 16&0xff # <<<<<<<<<<<<<<
- * call._coverage = self.iter.n_plp
+ /* "csamtools.pyx":2930
*
- */
- __pyx_v_call->_rms_mapping_quality = ((__pyx_v_cns >> 16) & 0xff);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3017
- * call._snp_quality = cns & 0xff
- * call._rms_mapping_quality = cns >> 16&0xff
- * call._coverage = self.iter.n_plp # <<<<<<<<<<<<<<
+ * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ * pos += l # <<<<<<<<<<<<<<
*
- * return call
+ * return overlap
*/
- __pyx_v_call->_coverage = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)__pyx_v_self)->__pyx_base.iter->n_plp;
+ __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_7, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_9 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_v_pos = __pyx_t_9;
+ break;
+ }
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3019
- * call._coverage = self.iter.n_plp
+ /* "csamtools.pyx":2932
+ * pos += l
*
- * return call # <<<<<<<<<<<<<<
+ * return overlap # <<<<<<<<<<<<<<
*
- * cdef class SNPCaller( SNPCallerBase ):
+ * def opt(self, tag):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_call));
- __pyx_r = ((PyObject *)__pyx_v_call);
+ __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_overlap); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_r = __pyx_t_5;
+ __pyx_t_5 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IteratorSNPCalls.__next__");
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_AddTraceback("csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF((PyObject *)__pyx_v_call);
+ __Pyx_XDECREF(__pyx_v_l);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3035
- *
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * IteratorColumn iterator_column,
- * **kwargs ):
- */
-
-static int __pyx_pf_9csamtools_9SNPCaller___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_9SNPCaller___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_iterator_column = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__iterator_column,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 3035);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__iterator_column);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3035; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)PyTuple_GET_ITEM(__pyx_args, 0));
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3035; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.SNPCaller.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_iterator_column), __pyx_ptype_9csamtools_IteratorColumn, 1, "iterator_column", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.SNPCaller.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_12opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("opt (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12opt(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tag));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3041
- * pass
+/* "csamtools.pyx":2934
+ * return overlap
*
- * def call(self, reference, int pos ): # <<<<<<<<<<<<<<
- * """call a snp on chromosome *reference*
- * and position *pos*.
+ * def opt(self, tag): # <<<<<<<<<<<<<<
+ * """retrieves optional data given a two-letter *tag*"""
+ * #see bam_aux.c: bam_aux_get() and bam_aux2i() etc
*/
-static PyObject *__pyx_pf_9csamtools_9SNPCaller_call(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_9SNPCaller_call[] = "SNPCaller.call(self, reference, int pos)\ncall a snp on chromosome *reference*\n and position *pos*.\n\n returns a :class:`SNPCall` object.\n ";
-static PyObject *__pyx_pf_9csamtools_9SNPCaller_call(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_reference = 0;
- int __pyx_v_pos;
- int __pyx_v_tid;
- char *__pyx_v_seq;
- int __pyx_v_seq_len;
- int __pyx_v_rb;
- uint32_t __pyx_v_cns;
- glf1_t *__pyx_v_g;
- struct __pyx_obj_9csamtools_SNPCall *__pyx_v_call;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag) {
+ uint8_t *__pyx_v_v;
+ CYTHON_UNUSED int __pyx_v_nvalues;
+ PyObject *__pyx_v_btag = NULL;
+ PyObject *__pyx_v_auxtype = NULL;
+ CYTHON_UNUSED PyObject *__pyx_v_bytesize = NULL;
+ PyObject *__pyx_v_values = NULL;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
+ char *__pyx_t_2;
+ int __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_5;
int __pyx_t_6;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__pos,0};
+ int __pyx_t_7;
+ int __pyx_t_8;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ PyObject *(*__pyx_t_12)(PyObject *);
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("call");
- __Pyx_TraceCall("call", __pyx_f[0], 3041);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("call", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3041; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "call") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3041; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_reference = values[0];
- __pyx_v_pos = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_pos == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3041; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_pos = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_pos == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3041; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("call", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3041; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.SNPCaller.call");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
- __pyx_v_call = ((struct __pyx_obj_9csamtools_SNPCall *)Py_None); __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3048
- * """
- *
- * cdef int tid = self.iter.samfile.gettid( reference ) # <<<<<<<<<<<<<<
- *
- * self.iter.reset( tid, pos, pos + 1 )
- */
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->samfile), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
- __Pyx_GIVEREF(__pyx_v_reference);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_tid = __pyx_t_4;
+ __Pyx_RefNannySetupContext("opt", 0);
+ __Pyx_TraceCall("opt", __pyx_f[0], 2934);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3050
- * cdef int tid = self.iter.samfile.gettid( reference )
- *
- * self.iter.reset( tid, pos, pos + 1 ) # <<<<<<<<<<<<<<
- *
- * while 1:
+ /* "csamtools.pyx":2939
+ * cdef uint8_t * v
+ * cdef int nvalues
+ * btag = _force_bytes(tag) # <<<<<<<<<<<<<<
+ * v = bam_aux_get(self._delegate, btag)
+ * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyInt_FromLong((__pyx_v_pos + 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_tag)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->reset(((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter, __pyx_t_3, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_v_btag = ((PyObject*)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3052
- * self.iter.reset( tid, pos, pos + 1 )
- *
- * while 1: # <<<<<<<<<<<<<<
- * self.iter.cnext()
- *
+ /* "csamtools.pyx":2940
+ * cdef int nvalues
+ * btag = _force_bytes(tag)
+ * v = bam_aux_get(self._delegate, btag) # <<<<<<<<<<<<<<
+ * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
+ * auxtype = chr(v[0])
*/
- while (1) {
- if (!1) break;
+ __pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_btag)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_v = bam_aux_get(__pyx_v_self->_delegate, __pyx_t_2);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3053
- *
- * while 1:
- * self.iter.cnext() # <<<<<<<<<<<<<<
- *
- * if self.iter.n_plp < 0:
+ /* "csamtools.pyx":2941
+ * btag = _force_bytes(tag)
+ * v = bam_aux_get(self._delegate, btag)
+ * if v == NULL: raise KeyError( "tag '%s' not present" % tag ) # <<<<<<<<<<<<<<
+ * auxtype = chr(v[0])
+ * if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter);
+ __pyx_t_3 = (__pyx_v_v == NULL);
+ if (__pyx_t_3) {
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_148), __pyx_v_tag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3055
- * self.iter.cnext()
- *
- * if self.iter.n_plp < 0: # <<<<<<<<<<<<<<
- * raise ValueError("error during iteration" )
- *
+ /* "csamtools.pyx":2942
+ * v = bam_aux_get(self._delegate, btag)
+ * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
+ * auxtype = chr(v[0]) # <<<<<<<<<<<<<<
+ * if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
+ * return <int>bam_aux2i(v)
*/
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->n_plp < 0);
- if (__pyx_t_6) {
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_chr, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_v_auxtype = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3056
- *
- * if self.iter.n_plp < 0:
- * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
- *
- * if self.iter.plp == NULL:
+ /* "csamtools.pyx":2943
+ * if v == NULL: raise KeyError( "tag '%s' not present" % tag )
+ * auxtype = chr(v[0])
+ * if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S': # <<<<<<<<<<<<<<
+ * return <int>bam_aux2i(v)
+ * elif auxtype == 'i' or auxtype == 'I':
*/
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3056; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_59));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_59));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_59));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3056; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3056; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
- }
- __pyx_L8:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3058
- * raise ValueError("error during iteration" )
- *
- * if self.iter.plp == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "no reads in region - no call" )
- *
- */
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->plp == NULL);
- if (__pyx_t_6) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3059
- *
- * if self.iter.plp == NULL:
- * raise ValueError( "no reads in region - no call" ) # <<<<<<<<<<<<<<
- *
- * if self.iter.pos == pos: break
- */
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_109));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_109));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_109));
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
- }
- __pyx_L9:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3061
- * raise ValueError( "no reads in region - no call" )
- *
- * if self.iter.pos == pos: break # <<<<<<<<<<<<<<
- *
- * cdef char * seq = self.iter.getSequence()
- */
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->pos == __pyx_v_pos);
- if (__pyx_t_6) {
- goto __pyx_L7_break;
- goto __pyx_L10;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__c), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_3) {
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__C), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_5) {
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__s), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_6) {
+ __pyx_t_7 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__S), Py_EQ); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __pyx_t_7;
+ } else {
+ __pyx_t_8 = __pyx_t_6;
+ }
+ __pyx_t_6 = __pyx_t_8;
+ } else {
+ __pyx_t_6 = __pyx_t_5;
}
- __pyx_L10:;
+ __pyx_t_5 = __pyx_t_6;
+ } else {
+ __pyx_t_5 = __pyx_t_3;
}
- __pyx_L7_break:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3063
- * if self.iter.pos == pos: break
- *
- * cdef char * seq = self.iter.getSequence() # <<<<<<<<<<<<<<
- * cdef int seq_len = self.iter.seq_len
- *
- */
- __pyx_v_seq = ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->getSequence(((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3064
- *
- * cdef char * seq = self.iter.getSequence()
- * cdef int seq_len = self.iter.seq_len # <<<<<<<<<<<<<<
- *
- * assert seq != NULL
- */
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter), __pyx_n_s__seq_len); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_5); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_v_seq_len = __pyx_t_4;
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3066
- * cdef int seq_len = self.iter.seq_len
- *
- * assert seq != NULL # <<<<<<<<<<<<<<
- *
- * # reference base
+ /* "csamtools.pyx":2944
+ * auxtype = chr(v[0])
+ * if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
+ * return <int>bam_aux2i(v) # <<<<<<<<<<<<<<
+ * elif auxtype == 'i' or auxtype == 'I':
+ * return <int32_t>bam_aux2i(v)
*/
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_seq != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
}
- #endif
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3069
- *
- * # reference base
- * if self.iter.pos >= seq_len: # <<<<<<<<<<<<<<
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
- *
+ /* "csamtools.pyx":2945
+ * if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
+ * return <int>bam_aux2i(v)
+ * elif auxtype == 'i' or auxtype == 'I': # <<<<<<<<<<<<<<
+ * return <int32_t>bam_aux2i(v)
+ * elif auxtype == 'f' or auxtype == 'F':
*/
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->pos >= __pyx_v_seq_len);
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__i), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_5) {
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__I), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __pyx_t_3;
+ } else {
+ __pyx_t_6 = __pyx_t_5;
+ }
if (__pyx_t_6) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3070
- * # reference base
- * if self.iter.pos >= seq_len:
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) ) # <<<<<<<<<<<<<<
- *
- * cdef int rb = seq[self.iter.pos]
+ /* "csamtools.pyx":2946
+ * return <int>bam_aux2i(v)
+ * elif auxtype == 'i' or auxtype == 'I':
+ * return <int32_t>bam_aux2i(v) # <<<<<<<<<<<<<<
+ * elif auxtype == 'f' or auxtype == 'F':
+ * return <float>bam_aux2f(v)
*/
- __pyx_t_5 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->pos); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_5 = 0;
- __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ goto __pyx_L0;
+ goto __pyx_L4;
}
- __pyx_L11:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3072
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
- *
- * cdef int rb = seq[self.iter.pos] # <<<<<<<<<<<<<<
- * cdef uint32_t cns
- * cdef glf1_t * g
- */
- __pyx_v_rb = (__pyx_v_seq[((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->pos]);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3079
- * self.iter.plp,
- * bam_nt16_table[rb],
- * self.c ) # <<<<<<<<<<<<<<
- *
- *
- */
- __pyx_v_g = bam_maqcns_glfgen(((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->n_plp, ((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->plp, (bam_nt16_table[__pyx_v_rb]), ((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.c);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3082
- *
- *
- * if pysam_glf_depth( g ) == 0: # <<<<<<<<<<<<<<
- * cns = 0xfu << 28 | 0xf << 24
- * else:
- */
- __pyx_t_6 = (pysam_glf_depth(__pyx_v_g) == 0);
- if (__pyx_t_6) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3083
- *
- * if pysam_glf_depth( g ) == 0:
- * cns = 0xfu << 28 | 0xf << 24 # <<<<<<<<<<<<<<
- * else:
- * cns = glf2cns(g, <int>(self.c.q_r + .499))
+ /* "csamtools.pyx":2947
+ * elif auxtype == 'i' or auxtype == 'I':
+ * return <int32_t>bam_aux2i(v)
+ * elif auxtype == 'f' or auxtype == 'F': # <<<<<<<<<<<<<<
+ * return <float>bam_aux2f(v)
+ * elif auxtype == 'd' or auxtype == 'D':
*/
- __pyx_v_cns = 4278190080U;
- goto __pyx_L12;
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__f), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_6) {
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__F), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __pyx_t_5;
+ } else {
+ __pyx_t_3 = __pyx_t_6;
}
- /*else*/ {
+ if (__pyx_t_3) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3085
- * cns = 0xfu << 28 | 0xf << 24
- * else:
- * cns = glf2cns(g, <int>(self.c.q_r + .499)) # <<<<<<<<<<<<<<
- *
- * free(g)
+ /* "csamtools.pyx":2948
+ * return <int32_t>bam_aux2i(v)
+ * elif auxtype == 'f' or auxtype == 'F':
+ * return <float>bam_aux2f(v) # <<<<<<<<<<<<<<
+ * elif auxtype == 'd' or auxtype == 'D':
+ * return <double>bam_aux2d(v)
*/
- __pyx_v_cns = glf2cns(__pyx_v_g, ((int)(((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.c->q_r + .499)));
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
}
- __pyx_L12:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3087
- * cns = glf2cns(g, <int>(self.c.q_r + .499))
- *
- * free(g) # <<<<<<<<<<<<<<
- *
- * cdef SNPCall call
- */
- free(__pyx_v_g);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3091
- * cdef SNPCall call
- *
- * call = SNPCall() # <<<<<<<<<<<<<<
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos
+ /* "csamtools.pyx":2949
+ * elif auxtype == 'f' or auxtype == 'F':
+ * return <float>bam_aux2f(v)
+ * elif auxtype == 'd' or auxtype == 'D': # <<<<<<<<<<<<<<
+ * return <double>bam_aux2d(v)
+ * elif auxtype == 'A':
*/
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_SNPCall)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_v_call));
- __pyx_v_call = ((struct __pyx_obj_9csamtools_SNPCall *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__d), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_3) {
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__D), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __pyx_t_6;
+ } else {
+ __pyx_t_5 = __pyx_t_3;
+ }
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3092
- *
- * call = SNPCall()
- * call._tid = self.iter.tid # <<<<<<<<<<<<<<
- * call._pos = self.iter.pos
- * call._reference_base = rb
+ /* "csamtools.pyx":2950
+ * return <float>bam_aux2f(v)
+ * elif auxtype == 'd' or auxtype == 'D':
+ * return <double>bam_aux2d(v) # <<<<<<<<<<<<<<
+ * elif auxtype == 'A':
+ * # there might a more efficient way
*/
- __pyx_v_call->_tid = ((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->tid;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3093
- * call = SNPCall()
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos # <<<<<<<<<<<<<<
- * call._reference_base = rb
- * call._genotype = bam_nt16_rev_table[cns>>28]
+ /* "csamtools.pyx":2951
+ * elif auxtype == 'd' or auxtype == 'D':
+ * return <double>bam_aux2d(v)
+ * elif auxtype == 'A': # <<<<<<<<<<<<<<
+ * # there might a more efficient way
+ * # to convert a char into a string
*/
- __pyx_v_call->_pos = ((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->pos;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3094
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos
- * call._reference_base = rb # <<<<<<<<<<<<<<
- * call._genotype = bam_nt16_rev_table[cns>>28]
- * call._consensus_quality = cns >> 8 & 0xff
+ /* "csamtools.pyx":2954
+ * # there might a more efficient way
+ * # to convert a char into a string
+ * return '%c' % <char>bam_aux2A(v) # <<<<<<<<<<<<<<
+ * elif auxtype == 'Z':
+ * return _charptr_to_str(<char*>bam_aux2Z(v))
*/
- __pyx_v_call->_reference_base = __pyx_v_rb;
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_4);
+ __pyx_t_4 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3095
- * call._pos = self.iter.pos
- * call._reference_base = rb
- * call._genotype = bam_nt16_rev_table[cns>>28] # <<<<<<<<<<<<<<
- * call._consensus_quality = cns >> 8 & 0xff
- * call._snp_quality = cns & 0xff
+ /* "csamtools.pyx":2955
+ * # to convert a char into a string
+ * return '%c' % <char>bam_aux2A(v)
+ * elif auxtype == 'Z': # <<<<<<<<<<<<<<
+ * return _charptr_to_str(<char*>bam_aux2Z(v))
+ * elif auxtype == 'B':
*/
- __pyx_v_call->_genotype = (__pyx_v_9csamtools_bam_nt16_rev_table[(__pyx_v_cns >> 28)]);
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__Z), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3096
- * call._reference_base = rb
- * call._genotype = bam_nt16_rev_table[cns>>28]
- * call._consensus_quality = cns >> 8 & 0xff # <<<<<<<<<<<<<<
- * call._snp_quality = cns & 0xff
- * call._rms_mapping_quality = cns >> 16&0xff
+ /* "csamtools.pyx":2956
+ * return '%c' % <char>bam_aux2A(v)
+ * elif auxtype == 'Z':
+ * return _charptr_to_str(<char*>bam_aux2Z(v)) # <<<<<<<<<<<<<<
+ * elif auxtype == 'B':
+ * bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
*/
- __pyx_v_call->_consensus_quality = ((__pyx_v_cns >> 8) & 0xff);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_4 = __pyx_f_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_v))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_r = __pyx_t_4;
+ __pyx_t_4 = 0;
+ goto __pyx_L0;
+ goto __pyx_L4;
+ }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3097
- * call._genotype = bam_nt16_rev_table[cns>>28]
- * call._consensus_quality = cns >> 8 & 0xff
- * call._snp_quality = cns & 0xff # <<<<<<<<<<<<<<
- * call._rms_mapping_quality = cns >> 16&0xff
- * call._coverage = self.iter.n_plp
+ /* "csamtools.pyx":2957
+ * elif auxtype == 'Z':
+ * return _charptr_to_str(<char*>bam_aux2Z(v))
+ * elif auxtype == 'B': # <<<<<<<<<<<<<<
+ * bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
+ * return values
*/
- __pyx_v_call->_snp_quality = (__pyx_v_cns & 0xff);
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__B), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3098
- * call._consensus_quality = cns >> 8 & 0xff
- * call._snp_quality = cns & 0xff
- * call._rms_mapping_quality = cns >> 16&0xff # <<<<<<<<<<<<<<
- * call._coverage = self.iter.n_plp
- *
+ /* "csamtools.pyx":2958
+ * return _charptr_to_str(<char*>bam_aux2Z(v))
+ * elif auxtype == 'B':
+ * bytesize, nvalues, values = convertBinaryTagToList( v + 1 ) # <<<<<<<<<<<<<<
+ * return values
+ * else:
*/
- __pyx_v_call->_rms_mapping_quality = ((__pyx_v_cns >> 16) & 0xff);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3099
- * call._snp_quality = cns & 0xff
- * call._rms_mapping_quality = cns >> 16&0xff
- * call._coverage = self.iter.n_plp # <<<<<<<<<<<<<<
- *
- * return call
+ __pyx_t_4 = __pyx_f_9csamtools_convertBinaryTagToList((__pyx_v_v + 1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
+ PyObject* sequence = __pyx_t_4;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
+ if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_10 = PyTuple_GET_ITEM(sequence, 2);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
+ if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_10 = PyList_GET_ITEM(sequence, 2);
+ }
+ __Pyx_INCREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_11 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
+ index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_10);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L6_unpacking_done;
+ __pyx_L5_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L6_unpacking_done:;
+ }
+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_v_bytesize = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __pyx_v_nvalues = __pyx_t_13;
+ __pyx_v_values = __pyx_t_10;
+ __pyx_t_10 = 0;
+
+ /* "csamtools.pyx":2959
+ * elif auxtype == 'B':
+ * bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
+ * return values # <<<<<<<<<<<<<<
+ * else:
+ * raise ValueError("unknown auxilliary type '%s'" % auxtype)
*/
- __pyx_v_call->_coverage = ((struct __pyx_obj_9csamtools_SNPCaller *)__pyx_v_self)->__pyx_base.iter->n_plp;
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(__pyx_v_values);
+ __pyx_r = __pyx_v_values;
+ goto __pyx_L0;
+ goto __pyx_L4;
+ }
+ /*else*/ {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3101
- * call._coverage = self.iter.n_plp
+ /* "csamtools.pyx":2961
+ * return values
+ * else:
+ * raise ValueError("unknown auxilliary type '%s'" % auxtype) # <<<<<<<<<<<<<<
*
- * return call # <<<<<<<<<<<<<<
*
- * cdef class IndelCall:
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_call));
- __pyx_r = ((PyObject *)__pyx_v_call);
- goto __pyx_L0;
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_149), __pyx_v_auxtype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_Raise(__pyx_t_4, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L4:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.SNPCaller.call");
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_AddTraceback("csamtools.AlignedRead.opt", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF((PyObject *)__pyx_v_call);
+ __Pyx_XDECREF(__pyx_v_btag);
+ __Pyx_XDECREF(__pyx_v_auxtype);
+ __Pyx_XDECREF(__pyx_v_bytesize);
+ __Pyx_XDECREF(__pyx_v_values);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3111
- * cdef bam_maqindel_ret_t * _r
- *
- * def __cinit__(self): # <<<<<<<<<<<<<<
- * #assert r != NULL
- * #self._r = r
- */
-
-static int __pyx_pf_9csamtools_9IndelCall___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_9IndelCall___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 3111);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
-
- __pyx_r = 0;
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_14fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
+static PyObject *__pyx_pw_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("fancy_str (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14fancy_str(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3118
- * property tid:
- * '''the chromosome ID as is defined in the header'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * return self._tid
+/* "csamtools.pyx":2964
*
+ *
+ * def fancy_str (self): # <<<<<<<<<<<<<<
+ * """returns list of fieldnames/values in pretty format for debugging
+ * """
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_3tid___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_v_ret_string = NULL;
+ PyObject *__pyx_v_field_names = NULL;
+ PyObject *__pyx_v_fields_names_in_order = NULL;
+ PyObject *__pyx_v_f = NULL;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ Py_ssize_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ int __pyx_t_10;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3118);
+ __Pyx_RefNannySetupContext("fancy_str", 0);
+ __Pyx_TraceCall("fancy_str", __pyx_f[0], 2964);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3119
- * '''the chromosome ID as is defined in the header'''
- * def __get__(self):
- * return self._tid # <<<<<<<<<<<<<<
- *
- * property pos:
+ /* "csamtools.pyx":2967
+ * """returns list of fieldnames/values in pretty format for debugging
+ * """
+ * ret_string = [] # <<<<<<<<<<<<<<
+ * field_names = {
+ * "tid": "Contig index",
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
+ __pyx_v_ret_string = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L0;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ /* "csamtools.pyx":2968
+ * """
+ * ret_string = []
+ * field_names = { # <<<<<<<<<<<<<<
+ * "tid": "Contig index",
+ * "pos": "Mapped position on contig",
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__tid), ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mtid), ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mpos), ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__isize), ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__flag), ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__n_cigar), ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__cigar), ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bin), ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qname), ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qname), ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qseq), ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qseq), ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bqual), ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_aux), ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__m_data), ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__data_len), ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_field_names = __pyx_t_1;
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2988
+ * "data_len": "Current data length",
+ * }
+ * fields_names_in_order = ["tid", "pos", "mtid", "mpos", "isize", "flag", # <<<<<<<<<<<<<<
+ * "n_cigar", "cigar", "qual", "bin", "l_qname", "qname",
+ * "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
+ */
+ __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__tid));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tid));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__tid));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__pos));
+ PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__pos));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__mtid));
+ PyList_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__mtid));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__mtid));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__mpos));
+ PyList_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__mpos));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__mpos));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__isize));
+ PyList_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__isize));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__isize));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__flag));
+ PyList_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__flag));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__flag));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__n_cigar));
+ PyList_SET_ITEM(__pyx_t_1, 6, ((PyObject *)__pyx_n_s__n_cigar));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n_cigar));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__cigar));
+ PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__cigar));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cigar));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__qual));
+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__qual));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qual));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__bin));
+ PyList_SET_ITEM(__pyx_t_1, 9, ((PyObject *)__pyx_n_s__bin));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__bin));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__l_qname));
+ PyList_SET_ITEM(__pyx_t_1, 10, ((PyObject *)__pyx_n_s__l_qname));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l_qname));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__qname));
+ PyList_SET_ITEM(__pyx_t_1, 11, ((PyObject *)__pyx_n_s__qname));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qname));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__l_qseq));
+ PyList_SET_ITEM(__pyx_t_1, 12, ((PyObject *)__pyx_n_s__l_qseq));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l_qseq));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__qseq));
+ PyList_SET_ITEM(__pyx_t_1, 13, ((PyObject *)__pyx_n_s__qseq));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qseq));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__bqual));
+ PyList_SET_ITEM(__pyx_t_1, 14, ((PyObject *)__pyx_n_s__bqual));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__bqual));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__l_aux));
+ PyList_SET_ITEM(__pyx_t_1, 15, ((PyObject *)__pyx_n_s__l_aux));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l_aux));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__m_data));
+ PyList_SET_ITEM(__pyx_t_1, 16, ((PyObject *)__pyx_n_s__m_data));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__m_data));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__data_len));
+ PyList_SET_ITEM(__pyx_t_1, 17, ((PyObject *)__pyx_n_s__data_len));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data_len));
+ __pyx_v_fields_names_in_order = __pyx_t_1;
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2992
+ * "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
+ *
+ * for f in fields_names_in_order: # <<<<<<<<<<<<<<
+ * if not f in self.__dict__:
+ * continue
+ */
+ __pyx_t_1 = ((PyObject *)__pyx_v_fields_names_in_order); __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
+ for (;;) {
+ if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
+ __Pyx_XDECREF(__pyx_v_f);
+ __pyx_v_f = __pyx_t_3;
+ __pyx_t_3 = 0;
+
+ /* "csamtools.pyx":2993
+ *
+ * for f in fields_names_in_order:
+ * if not f in self.__dict__: # <<<<<<<<<<<<<<
+ * continue
+ * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
+ */
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = ((PySequence_Contains(__pyx_t_3, __pyx_v_f))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_5 = (!__pyx_t_4);
+ if (__pyx_t_5) {
+
+ /* "csamtools.pyx":2994
+ * for f in fields_names_in_order:
+ * if not f in self.__dict__:
+ * continue # <<<<<<<<<<<<<<
+ * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
+ *
+ */
+ goto __pyx_L3_continue;
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
+
+ /* "csamtools.pyx":2995
+ * if not f in self.__dict__:
+ * continue
+ * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f))) # <<<<<<<<<<<<<<
+ *
+ * for f in self.__dict__:
+ */
+ __pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_field_names), __pyx_v_f); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_kp_s_169), __pyx_v_f); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyNumber_Add(__pyx_t_6, ((PyObject *)__pyx_kp_s_170)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
+ __Pyx_GIVEREF(__pyx_v_f);
+ __pyx_t_9 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_3 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_168), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_L3_continue:;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2997
+ * ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
+ *
+ * for f in self.__dict__: # <<<<<<<<<<<<<<
+ * if not f in field_names:
+ * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
+ */
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_9 = __pyx_t_1; __Pyx_INCREF(__pyx_t_9); __pyx_t_2 = 0;
+ __pyx_t_11 = NULL;
+ } else {
+ __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_11 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ for (;;) {
+ if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
+ } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
+ } else {
+ __pyx_t_1 = __pyx_t_11(__pyx_t_9);
+ if (unlikely(!__pyx_t_1)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_1);
+ }
+ __Pyx_XDECREF(__pyx_v_f);
+ __pyx_v_f = __pyx_t_1;
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":2998
+ *
+ * for f in self.__dict__:
+ * if not f in field_names: # <<<<<<<<<<<<<<
+ * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
+ * return ret_string
+ */
+ __pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (!__pyx_t_5);
+ if (__pyx_t_4) {
+
+ /* "csamtools.pyx":2999
+ * for f in self.__dict__:
+ * if not f in field_names:
+ * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f))) # <<<<<<<<<<<<<<
+ * return ret_string
+ *
+ */
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
+ __Pyx_GIVEREF(__pyx_v_f);
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
+ __Pyx_GIVEREF(__pyx_v_f);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_16));
+ PyTuple_SET_ITEM(__pyx_t_8, 1, ((PyObject *)__pyx_kp_s_16));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_16));
+ PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_168), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
+ }
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+
+ /* "csamtools.pyx":3000
+ * if not f in field_names:
+ * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
+ * return ret_string # <<<<<<<<<<<<<<
+ *
+ * cdef class PileupProxy:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_ret_string));
+ __pyx_r = ((PyObject *)__pyx_v_ret_string);
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.tid.__get__");
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_AddTraceback("csamtools.AlignedRead.fancy_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_ret_string);
+ __Pyx_XDECREF(__pyx_v_field_names);
+ __Pyx_XDECREF(__pyx_v_fields_names_in_order);
+ __Pyx_XDECREF(__pyx_v_f);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3123
- * property pos:
- * '''nucleotide position of SNP.'''
- * def __get__(self): return self._pos # <<<<<<<<<<<<<<
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy___init__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3019
+ * will change.
+ * '''
+ * def __init__(self): # <<<<<<<<<<<<<<
+ * raise TypeError("This class cannot be instantiated from Python")
*
- * property genotype:
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_3pos___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
+static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3123);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3019);
+
+ /* "csamtools.pyx":3020
+ * '''
+ * def __init__(self):
+ * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
+ *
+ * def __str__(self):
+ */
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_TypeError, ((PyObject *)__pyx_k_tuple_172), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.pos.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.PileupProxy.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3127
- * property genotype:
- * '''the genotype called.'''
- * def __get__(self): # <<<<<<<<<<<<<<
- * if self._r.gt == 0:
- * s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy_2__str__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3022
+ * raise TypeError("This class cannot be instantiated from Python")
+ *
+ * def __str__(self): # <<<<<<<<<<<<<<
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" +\
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_8genotype___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_8genotype___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_v_s;
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3127);
- __pyx_v_s = Py_None; __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3128
- * '''the genotype called.'''
- * def __get__(self):
- * if self._r.gt == 0: # <<<<<<<<<<<<<<
- * s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
- * return "%s/%s" % (s,s)
- */
- switch (((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->gt) {
- case 0:
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3129
- * def __get__(self):
- * if self._r.gt == 0:
- * s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1) # <<<<<<<<<<<<<<
- * return "%s/%s" % (s,s)
- * elif self._r.gt == 1:
- */
- __pyx_t_1 = PyString_FromStringAndSize((((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->s[0]), (((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->indel1 + 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_v_s);
- __pyx_v_s = __pyx_t_1;
- __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3130
- * if self._r.gt == 0:
- * s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
- * return "%s/%s" % (s,s) # <<<<<<<<<<<<<<
- * elif self._r.gt == 1:
- * s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
- */
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_v_s);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_s);
- __Pyx_GIVEREF(__pyx_v_s);
- __Pyx_INCREF(__pyx_v_s);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_s);
- __Pyx_GIVEREF(__pyx_v_s);
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
- goto __pyx_L0;
- break;
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 3022);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3131
- * s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1)
- * return "%s/%s" % (s,s)
- * elif self._r.gt == 1: # <<<<<<<<<<<<<<
- * s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
- * return "%s/%s" % (s,s)
+ /* "csamtools.pyx":3023
+ *
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
+ * "\n" +\
+ * "\n".join( map(str, self.pileups) )
*/
- case 1:
+ __Pyx_XDECREF(__pyx_r);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3132
- * return "%s/%s" % (s,s)
- * elif self._r.gt == 1:
- * s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1) # <<<<<<<<<<<<<<
- * return "%s/%s" % (s,s)
- * else:
+ /* "csamtools.pyx":3024
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" +\ # <<<<<<<<<<<<<<
+ * "\n".join( map(str, self.pileups) )
+ *
*/
- __pyx_t_2 = PyString_FromStringAndSize((((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->s[1]), (((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->indel2 + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_v_s);
- __pyx_v_s = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3133
- * elif self._r.gt == 1:
- * s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1)
- * return "%s/%s" % (s,s) # <<<<<<<<<<<<<<
- * else:
- * return "%s/%s" % (self.first_allele, self.second_allele )
+ /* "csamtools.pyx":3023
+ *
+ * def __str__(self):
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
+ * "\n" +\
+ * "\n".join( map(str, self.pileups) )
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_s);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_s);
- __Pyx_GIVEREF(__pyx_v_s);
- __Pyx_INCREF(__pyx_v_s);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_s);
- __Pyx_GIVEREF(__pyx_v_s);
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
- goto __pyx_L0;
- break;
- default:
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_2 = 0;
+ __pyx_t_3 = 0;
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_4 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3135
- * return "%s/%s" % (s,s)
- * else:
- * return "%s/%s" % (self.first_allele, self.second_allele ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3025
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" +\
+ * "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
*
- * property consensus_quality:
+ * property tid:
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__first_allele); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__second_allele); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_1 = 0;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
- goto __pyx_L0;
- break;
- }
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyNumber_Add(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
+ goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IndelCall.genotype.__get__");
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("csamtools.PileupProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_s);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3139
- * property consensus_quality:
- * '''the genotype quality (Phred-scaled).'''
- * def __get__(self): return self._r.q_cns # <<<<<<<<<<<<<<
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy_3tid___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3029
+ * property tid:
+ * '''the chromosome ID as is defined in the header'''
+ * def __get__(self): return self.tid # <<<<<<<<<<<<<<
*
- * property snp_quality:
+ * property n:
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_17consensus_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_17consensus_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3139);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3029);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->q_cns); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.consensus_quality.__get__");
+ __Pyx_AddTraceback("csamtools.PileupProxy.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3143
- * property snp_quality:
- * '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
- * def __get__(self): return self._r.q_ref # <<<<<<<<<<<<<<
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy_1n___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3033
+ * property n:
+ * '''number of reads mapping to this column.'''
+ * def __get__(self): return self.n_pu # <<<<<<<<<<<<<<
+ * def __set__(self, n): self.n_pu = n
*
- * property mapping_quality:
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_11snp_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_11snp_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3143);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3033);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->q_ref); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.snp_quality.__get__");
+ __Pyx_AddTraceback("csamtools.PileupProxy.n.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3147
- * property mapping_quality:
- * '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
- * def __get__(self): return self._rms_mapping_quality # <<<<<<<<<<<<<<
+/* Python wrapper */
+static int __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
+static int __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self), ((PyObject *)__pyx_v_n));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3034
+ * '''number of reads mapping to this column.'''
+ * def __get__(self): return self.n_pu
+ * def __set__(self, n): self.n_pu = n # <<<<<<<<<<<<<<
*
- * property coverage:
+ * property pos:
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_15mapping_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_15mapping_quality___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
+static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3147);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 3034);
+ __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_n); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->n_pu = __pyx_t_1;
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.mapping_quality.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.PileupProxy.n.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3151
- * property coverage:
- * '''coverage or read depth - the number of reads involved in the call.'''
- * def __get__(self): return self._coverage # <<<<<<<<<<<<<<
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy_3pos___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3037
+ *
+ * property pos:
+ * def __get__(self): return self.pos # <<<<<<<<<<<<<<
*
- * property first_allele:
+ * property pileups:
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_8coverage___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_8coverage___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3151);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3037);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.coverage.__get__");
+ __Pyx_AddTraceback("csamtools.PileupProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3155
- * property first_allele:
- * '''sequence of first allele.'''
- * def __get__(self): return PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1) # <<<<<<<<<<<<<<
- *
- * property second_allele:
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3041
+ * property pileups:
+ * '''list of reads (:class:`pysam.PileupRead`) aligned to this column'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * cdef int x
+ * pileups = []
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_12first_allele___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_12first_allele___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+ int __pyx_v_x;
+ PyObject *__pyx_v_pileups = NULL;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3155);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyString_FromStringAndSize((((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->s[0]), (((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->indel1 + 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3041);
+
+ /* "csamtools.pyx":3043
+ * def __get__(self):
+ * cdef int x
+ * pileups = [] # <<<<<<<<<<<<<<
+ *
+ * if self.plp[0] == NULL:
+ */
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
+ __pyx_v_pileups = __pyx_t_1;
__pyx_t_1 = 0;
+
+ /* "csamtools.pyx":3045
+ * pileups = []
+ *
+ * if self.plp[0] == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError("PileupProxy accessed after iterator finished")
+ *
+ */
+ __pyx_t_2 = ((__pyx_v_self->plp[0]) == NULL);
+ if (__pyx_t_2) {
+
+ /* "csamtools.pyx":3046
+ *
+ * if self.plp[0] == NULL:
+ * raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<<
+ *
+ * # warning: there could be problems if self.n and self.buf are
+ */
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_174), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":3050
+ * # warning: there could be problems if self.n and self.buf are
+ * # out of sync.
+ * for x from 0 <= x < self.n_pu: # <<<<<<<<<<<<<<
+ * pileups.append( makePileupRead( &(self.plp[0][x])) )
+ * return pileups
+ */
+ __pyx_t_3 = __pyx_v_self->n_pu;
+ for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
+
+ /* "csamtools.pyx":3051
+ * # out of sync.
+ * for x from 0 <= x < self.n_pu:
+ * pileups.append( makePileupRead( &(self.plp[0][x])) ) # <<<<<<<<<<<<<<
+ * return pileups
+ *
+ */
+ __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&((__pyx_v_self->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ }
+
+ /* "csamtools.pyx":3052
+ * for x from 0 <= x < self.n_pu:
+ * pileups.append( makePileupRead( &(self.plp[0][x])) )
+ * return pileups # <<<<<<<<<<<<<<
+ *
+ * cdef class PileupRead:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_pileups));
+ __pyx_r = ((PyObject *)__pyx_v_pileups);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.first_allele.__get__");
+ __Pyx_AddTraceback("csamtools.PileupProxy.pileups.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_pileups);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3159
- * property second_allele:
- * '''sequence of second allele.'''
- * def __get__(self): return PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1) # <<<<<<<<<<<<<<
- *
- * property reads_first:
- */
-
-static PyObject *__pyx_pf_9csamtools_9IndelCall_13second_allele___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_13second_allele___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3159);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyString_FromStringAndSize((((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->s[1]), (((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->indel2 + 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.second_allele.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+/* Python wrapper */
+static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead___init__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3163
- * property reads_first:
- * '''reads supporting first allele.'''
- * def __get__(self): return self._r.cnt1 # <<<<<<<<<<<<<<
+/* "csamtools.pyx":3058
+ * '''
+ *
+ * def __init__(self): # <<<<<<<<<<<<<<
+ * raise TypeError("This class cannot be instantiated from Python")
*
- * property reads_second:
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_11reads_first___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_11reads_first___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
+static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3163);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->cnt1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.reads_first.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3058);
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3167
- * property reads_second:
- * '''reads supporting first allele.'''
- * def __get__(self): return self._r.cnt2 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3059
*
- * property reads_diff:
+ * def __init__(self):
+ * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
+ *
+ * def __str__(self):
*/
-
-static PyObject *__pyx_pf_9csamtools_9IndelCall_12reads_second___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_12reads_second___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3167);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->cnt2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_TypeError, ((PyObject *)__pyx_k_tuple_175), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.reads_second.__get__");
- __pyx_r = NULL;
+ __Pyx_AddTraceback("csamtools.PileupRead.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
__pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3171
- * property reads_diff:
- * '''reads supporting first allele.'''
- * def __get__(self): return self._r.cnt_anti # <<<<<<<<<<<<<<
- *
- * def __str__(self):
- */
-
-static PyObject *__pyx_pf_9csamtools_9IndelCall_10reads_diff___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall_10reads_diff___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3171);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r->cnt_anti); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IndelCall.reads_diff.__get__");
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_2__str__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3173
- * def __get__(self): return self._r.cnt_anti
+/* "csamtools.pyx":3061
+ * raise TypeError("This class cannot be instantiated from Python")
*
* def __str__(self): # <<<<<<<<<<<<<<
+ * return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) )
*
- * return "\t".join( map(str, (
*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall___str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9IndelCall___str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- PyObject *__pyx_t_12 = NULL;
- PyObject *__pyx_t_13 = NULL;
- PyObject *__pyx_t_14 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 3173);
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 3061);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3175
+ /* "csamtools.pyx":3062
+ *
* def __str__(self):
+ * return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) ) # <<<<<<<<<<<<<<
*
- * return "\t".join( map(str, ( # <<<<<<<<<<<<<<
- * self.tid,
- * self.pos,
+ * property alignment:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3176
- *
- * return "\t".join( map(str, (
- * self.tid, # <<<<<<<<<<<<<<
- * self.pos,
- * self.genotype,
- */
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3177
- * return "\t".join( map(str, (
- * self.tid,
- * self.pos, # <<<<<<<<<<<<<<
- * self.genotype,
- * self.consensus_quality,
- */
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3178
- * self.tid,
- * self.pos,
- * self.genotype, # <<<<<<<<<<<<<<
- * self.consensus_quality,
- * self.snp_quality,
- */
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__genotype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3179
- * self.pos,
- * self.genotype,
- * self.consensus_quality, # <<<<<<<<<<<<<<
- * self.snp_quality,
- * self.mapping_quality,
- */
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3180
- * self.genotype,
- * self.consensus_quality,
- * self.snp_quality, # <<<<<<<<<<<<<<
- * self.mapping_quality,
- * self.coverage,
- */
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3181
- * self.consensus_quality,
- * self.snp_quality,
- * self.mapping_quality, # <<<<<<<<<<<<<<
- * self.coverage,
- * self.first_allele,
- */
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3182
- * self.snp_quality,
- * self.mapping_quality,
- * self.coverage, # <<<<<<<<<<<<<<
- * self.first_allele,
- * self.second_allele,
- */
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__coverage); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3183
- * self.mapping_quality,
- * self.coverage,
- * self.first_allele, # <<<<<<<<<<<<<<
- * self.second_allele,
- * self.reads_first,
- */
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__first_allele); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3184
- * self.coverage,
- * self.first_allele,
- * self.second_allele, # <<<<<<<<<<<<<<
- * self.reads_first,
- * self.reads_second,
- */
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__second_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3185
- * self.first_allele,
- * self.second_allele,
- * self.reads_first, # <<<<<<<<<<<<<<
- * self.reads_second,
- * self.reads_diff ) ) )
- */
- __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reads_first); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3186
- * self.second_allele,
- * self.reads_first,
- * self.reads_second, # <<<<<<<<<<<<<<
- * self.reads_diff ) ) )
- *
- */
- __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reads_second); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3187
- * self.reads_first,
- * self.reads_second,
- * self.reads_diff ) ) ) # <<<<<<<<<<<<<<
- *
- * def __dealloc__(self ):
- */
- __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reads_diff); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_14 = PyTuple_New(12); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_14, 2, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_14, 3, __pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_9, 3, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_14, 4, __pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_9, 4, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_14, 5, __pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_9, 5, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_14, 6, __pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_9, 6, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_14, 7, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_14, 8, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_14, 9, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
- PyTuple_SET_ITEM(__pyx_t_14, 10, __pyx_t_12);
- __Pyx_GIVEREF(__pyx_t_12);
- PyTuple_SET_ITEM(__pyx_t_14, 11, __pyx_t_13);
- __Pyx_GIVEREF(__pyx_t_13);
__pyx_t_2 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_6 = 0;
__pyx_t_7 = 0;
__pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_8, 1, ((PyObject *)__pyx_t_9));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
- __pyx_t_10 = 0;
- __pyx_t_11 = 0;
- __pyx_t_12 = 0;
- __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(2); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)((PyObject*)&PyString_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyString_Type)));
- PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_builtin_map, __pyx_t_13, NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_1, __pyx_t_13, NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_r = __pyx_t_14;
- __pyx_t_14 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_r = __pyx_t_9;
+ __pyx_t_9 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_XDECREF(__pyx_t_12);
- __Pyx_XDECREF(__pyx_t_13);
- __Pyx_XDECREF(__pyx_t_14);
- __Pyx_AddTraceback("csamtools.IndelCall.__str__");
+ __Pyx_AddTraceback("csamtools.PileupRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3189
- * self.reads_diff ) ) )
- *
- * def __dealloc__(self ): # <<<<<<<<<<<<<<
- * bam_maqindel_ret_destroy(self._r)
- *
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_9alignment___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3066
+ * property alignment:
+ * """a :class:`pysam.AlignedRead` object of the aligned read"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._alignment
+ * property qpos:
*/
-static void __pyx_pf_9csamtools_9IndelCall___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_9IndelCall___dealloc__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3189);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3066);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3190
- *
- * def __dealloc__(self ):
- * bam_maqindel_ret_destroy(self._r) # <<<<<<<<<<<<<<
- *
- * cdef class IndelCallerBase:
+ /* "csamtools.pyx":3067
+ * """a :class:`pysam.AlignedRead` object of the aligned read"""
+ * def __get__(self):
+ * return self._alignment # <<<<<<<<<<<<<<
+ * property qpos:
+ * """position of the read base at the pileup site, 0-based"""
*/
- bam_maqindel_ret_destroy(((struct __pyx_obj_9csamtools_IndelCall *)__pyx_v_self)->_r);
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->_alignment));
+ __pyx_r = ((PyObject *)__pyx_v_self->_alignment);
+ goto __pyx_L0;
- __Pyx_TraceReturn(Py_None);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3212
- * cdef int max_depth
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * IteratorColumn iterator_column,
- * **kwargs ):
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_4qpos___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3070
+ * property qpos:
+ * """position of the read base at the pileup site, 0-based"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._qpos
+ * property indel:
*/
-static int __pyx_pf_9csamtools_15IndelCallerBase___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_15IndelCallerBase___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_iterator_column = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
+static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- float __pyx_t_4;
- int __pyx_t_5;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__iterator_column,0};
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 3212);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__iterator_column);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)PyTuple_GET_ITEM(__pyx_args, 0));
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IndelCallerBase.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_iterator_column), __pyx_ptype_9csamtools_IteratorColumn, 1, "iterator_column", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3070);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3217
- *
- *
- * self.iter = iterator_column # <<<<<<<<<<<<<<
- *
- * assert iterator_column.hasReference(), "IndelCallerBase requires an pileup iterator with reference sequence"
+ /* "csamtools.pyx":3071
+ * """position of the read base at the pileup site, 0-based"""
+ * def __get__(self):
+ * return self._qpos # <<<<<<<<<<<<<<
+ * property indel:
+ * """indel length; 0 for no indel, positive for ins and negative for del"""
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_iterator_column));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_iterator_column));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter));
- ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter = __pyx_v_iterator_column;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3219
- * self.iter = iterator_column
- *
- * assert iterator_column.hasReference(), "IndelCallerBase requires an pileup iterator with reference sequence" # <<<<<<<<<<<<<<
- *
- * self.options = bam_maqindel_opt_init()
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_iterator_column), __pyx_n_s__hasReference); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(!__pyx_t_3)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_111));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3221
- * assert iterator_column.hasReference(), "IndelCallerBase requires an pileup iterator with reference sequence"
- *
- * self.options = bam_maqindel_opt_init() # <<<<<<<<<<<<<<
- *
- * # set the default parameterization according to
- */
- ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->options = bam_maqindel_opt_init();
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.PileupRead.qpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3226
- * # samtools
- *
- * self.options.r_indel = kwargs.get( "r_indel", 0.00015 ) # <<<<<<<<<<<<<<
- * self.options.q_indel = kwargs.get( "q_indel", 40 )
- * self.cap_mapQ = kwargs.get( "cap_mapQ", 60 )
- */
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyFloat_FromDouble(0.00015); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__r_indel), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __pyx_PyFloat_AsDouble(__pyx_t_1); if (unlikely((__pyx_t_4 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->options->r_indel = __pyx_t_4;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_5indel___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3227
- *
- * self.options.r_indel = kwargs.get( "r_indel", 0.00015 )
- * self.options.q_indel = kwargs.get( "q_indel", 40 ) # <<<<<<<<<<<<<<
- * self.cap_mapQ = kwargs.get( "cap_mapQ", 60 )
- * self.max_depth = kwargs.get( "max_depth", 1024 )
+/* "csamtools.pyx":3074
+ * property indel:
+ * """indel length; 0 for no indel, positive for ins and negative for del"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._indel
+ * property is_del:
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__q_indel), __pyx_int_40); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->options->q_indel = __pyx_t_5;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3228
- * self.options.r_indel = kwargs.get( "r_indel", 0.00015 )
- * self.options.q_indel = kwargs.get( "q_indel", 40 )
- * self.cap_mapQ = kwargs.get( "cap_mapQ", 60 ) # <<<<<<<<<<<<<<
- * self.max_depth = kwargs.get( "max_depth", 1024 )
- *
- */
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__cap_mapQ), __pyx_int_60); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->cap_mapQ = __pyx_t_5;
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3074);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3229
- * self.options.q_indel = kwargs.get( "q_indel", 40 )
- * self.cap_mapQ = kwargs.get( "cap_mapQ", 60 )
- * self.max_depth = kwargs.get( "max_depth", 1024 ) # <<<<<<<<<<<<<<
- *
- * def __dealloc__(self):
+ /* "csamtools.pyx":3075
+ * """indel length; 0 for no indel, positive for ins and negative for del"""
+ * def __get__(self):
+ * return self._indel # <<<<<<<<<<<<<<
+ * property is_del:
+ * """1 iff the base on the padded read is a deletion"""
*/
- if (unlikely(__pyx_v_kwargs == Py_None)) {
- PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'get'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__max_depth), __pyx_int_1024); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3075; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->max_depth = __pyx_t_5;
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- __pyx_r = 0;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IndelCallerBase.__cinit__");
- __pyx_r = -1;
+ __Pyx_AddTraceback("csamtools.PileupRead.indel.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3231
- * self.max_depth = kwargs.get( "max_depth", 1024 )
- *
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * free( self.options )
- *
- */
-
-static void __pyx_pf_9csamtools_15IndelCallerBase___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_15IndelCallerBase___dealloc__(PyObject *__pyx_v_self) {
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3231);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3232
- *
- * def __dealloc__(self):
- * free( self.options ) # <<<<<<<<<<<<<<
- *
- * def _call( self ):
- */
- free(((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->options);
-
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_6is_del___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3234
- * free( self.options )
- *
- * def _call( self ): # <<<<<<<<<<<<<<
- *
- * cdef char * seq = self.iter.getSequence()
+/* "csamtools.pyx":3078
+ * property is_del:
+ * """1 iff the base on the padded read is a deletion"""
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._is_del
+ * property is_head:
*/
-static PyObject *__pyx_pf_9csamtools_15IndelCallerBase__call(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_15IndelCallerBase__call[] = "IndelCallerBase._call(self)";
-static PyObject *__pyx_pf_9csamtools_15IndelCallerBase__call(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- char *__pyx_v_seq;
- int __pyx_v_seq_len;
- bam_maqindel_ret_t *__pyx_v_r;
- int __pyx_v_m;
- struct __pyx_obj_9csamtools_IndelCall *__pyx_v_call;
- uint64_t __pyx_v_rms_aux;
- int __pyx_v_i;
- bam_pileup1_t *__pyx_v_p;
- int __pyx_v_tmp;
+static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- int __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- int __pyx_t_6;
- int __pyx_t_7;
- double __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_call");
- __Pyx_TraceCall("_call", __pyx_f[0], 3234);
- __pyx_v_call = ((struct __pyx_obj_9csamtools_IndelCall *)Py_None); __Pyx_INCREF(Py_None);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3236
- * def _call( self ):
- *
- * cdef char * seq = self.iter.getSequence() # <<<<<<<<<<<<<<
- * cdef int seq_len = self.iter.seq_len
- *
- */
- __pyx_v_seq = ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->__pyx_vtab)->getSequence(((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3078);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3237
- *
- * cdef char * seq = self.iter.getSequence()
- * cdef int seq_len = self.iter.seq_len # <<<<<<<<<<<<<<
- *
- * assert seq != NULL
+ /* "csamtools.pyx":3079
+ * """1 iff the base on the padded read is a deletion"""
+ * def __get__(self):
+ * return self._is_del # <<<<<<<<<<<<<<
+ * property is_head:
+ * def __get__(self):
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter), __pyx_n_s__seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_v_seq_len = __pyx_t_2;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3239
- * cdef int seq_len = self.iter.seq_len
- *
- * assert seq != NULL # <<<<<<<<<<<<<<
- *
- * # reference base
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_seq != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3242
- *
- * # reference base
- * if self.iter.pos >= seq_len: # <<<<<<<<<<<<<<
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) )
- *
- */
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->pos >= __pyx_v_seq_len);
- if (__pyx_t_3) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3243
- * # reference base
- * if self.iter.pos >= seq_len:
- * raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) ) # <<<<<<<<<<<<<<
- *
- * cdef bam_maqindel_ret_t * r
- */
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyInt_FromLong(__pyx_v_seq_len); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_1 = 0;
- __pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3247
- * cdef bam_maqindel_ret_t * r
- *
- * cdef int m = min( self.max_depth, self.iter.n_plp ) # <<<<<<<<<<<<<<
- *
- * # printf("pysam: m=%i, q_indel=%i, r_indel=%f, r_snp=%i, mm_penalty=%i, indel_err=%i, ambi_thres=%i\n",
- */
- __pyx_t_2 = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->n_plp;
- __pyx_t_6 = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->max_depth;
- if ((__pyx_t_2 < __pyx_t_6)) {
- __pyx_t_7 = __pyx_t_2;
- } else {
- __pyx_t_7 = __pyx_t_6;
- }
- __pyx_v_m = __pyx_t_7;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3259
- * seq,
- * 0,
- * NULL) # <<<<<<<<<<<<<<
- *
- * if r == NULL: return None
- */
- __pyx_v_r = bam_maqindel(__pyx_v_m, ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->pos, ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->options, ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->plp, __pyx_v_seq, 0, NULL);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3261
- * NULL)
- *
- * if r == NULL: return None # <<<<<<<<<<<<<<
- *
- * cdef IndelCall call
- */
- __pyx_t_3 = (__pyx_v_r == NULL);
- if (__pyx_t_3) {
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(Py_None);
- __pyx_r = Py_None;
- goto __pyx_L0;
- goto __pyx_L6;
- }
- __pyx_L6:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3264
- *
- * cdef IndelCall call
- * call = IndelCall() # <<<<<<<<<<<<<<
- * call._r = r
- * call._tid = self.iter.tid
- */
- __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IndelCall)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(((PyObject *)__pyx_v_call));
- __pyx_v_call = ((struct __pyx_obj_9csamtools_IndelCall *)__pyx_t_4);
- __pyx_t_4 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3265
- * cdef IndelCall call
- * call = IndelCall()
- * call._r = r # <<<<<<<<<<<<<<
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos
- */
- __pyx_v_call->_r = __pyx_v_r;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3266
- * call = IndelCall()
- * call._r = r
- * call._tid = self.iter.tid # <<<<<<<<<<<<<<
- * call._pos = self.iter.pos
- * call._coverage = self.iter.n_plp
- */
- __pyx_v_call->_tid = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->tid;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3267
- * call._r = r
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos # <<<<<<<<<<<<<<
- * call._coverage = self.iter.n_plp
- *
- */
- __pyx_v_call->_pos = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->pos;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3268
- * call._tid = self.iter.tid
- * call._pos = self.iter.pos
- * call._coverage = self.iter.n_plp # <<<<<<<<<<<<<<
- *
- * cdef uint64_t rms_aux = 0
- */
- __pyx_v_call->_coverage = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->n_plp;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3270
- * call._coverage = self.iter.n_plp
- *
- * cdef uint64_t rms_aux = 0 # <<<<<<<<<<<<<<
- * cdef int i = 0
- * cdef bam_pileup1_t * p
- */
- __pyx_v_rms_aux = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3271
- *
- * cdef uint64_t rms_aux = 0
- * cdef int i = 0 # <<<<<<<<<<<<<<
- * cdef bam_pileup1_t * p
- * cdef int tmp
- */
- __pyx_v_i = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3275
- * cdef int tmp
- *
- * for i from 0 <= i < self.iter.n_plp: # <<<<<<<<<<<<<<
- * p = self.iter.plp + i
- * if p.b.core.qual < self.cap_mapQ:
- */
- __pyx_t_7 = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->n_plp;
- for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3276
- *
- * for i from 0 <= i < self.iter.n_plp:
- * p = self.iter.plp + i # <<<<<<<<<<<<<<
- * if p.b.core.qual < self.cap_mapQ:
- * tmp = p.b.core.qual
- */
- __pyx_v_p = (((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->plp + __pyx_v_i);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3277
- * for i from 0 <= i < self.iter.n_plp:
- * p = self.iter.plp + i
- * if p.b.core.qual < self.cap_mapQ: # <<<<<<<<<<<<<<
- * tmp = p.b.core.qual
- * else:
- */
- __pyx_t_3 = (__pyx_v_p->b->core.qual < ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->cap_mapQ);
- if (__pyx_t_3) {
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3278
- * p = self.iter.plp + i
- * if p.b.core.qual < self.cap_mapQ:
- * tmp = p.b.core.qual # <<<<<<<<<<<<<<
- * else:
- * tmp = self.cap_mapQ
- */
- __pyx_v_tmp = __pyx_v_p->b->core.qual;
- goto __pyx_L9;
- }
- /*else*/ {
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.PileupRead.is_del.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3280
- * tmp = p.b.core.qual
- * else:
- * tmp = self.cap_mapQ # <<<<<<<<<<<<<<
- * rms_aux += tmp * tmp
- *
- */
- __pyx_v_tmp = ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->cap_mapQ;
- }
- __pyx_L9:;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_7is_head___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3281
- * else:
- * tmp = self.cap_mapQ
- * rms_aux += tmp * tmp # <<<<<<<<<<<<<<
- *
- * call._rms_mapping_quality = <uint64_t>(sqrt(<double>rms_aux / self.iter.n_plp) + .499)
+/* "csamtools.pyx":3081
+ * return self._is_del
+ * property is_head:
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._is_head
+ * property is_tail:
*/
- __pyx_v_rms_aux += (__pyx_v_tmp * __pyx_v_tmp);
- }
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3283
- * rms_aux += tmp * tmp
- *
- * call._rms_mapping_quality = <uint64_t>(sqrt(<double>rms_aux / self.iter.n_plp) + .499) # <<<<<<<<<<<<<<
- *
- * return call
- */
- __pyx_t_8 = ((double)__pyx_v_rms_aux);
- if (unlikely(((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->n_plp == 0)) {
- PyErr_Format(PyExc_ZeroDivisionError, "float division");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_v_call->_rms_mapping_quality = ((uint64_t)(sqrt((__pyx_t_8 / ((struct __pyx_obj_9csamtools_IndelCallerBase *)__pyx_v_self)->iter->n_plp)) + .499));
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3081);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3285
- * call._rms_mapping_quality = <uint64_t>(sqrt(<double>rms_aux / self.iter.n_plp) + .499)
- *
- * return call # <<<<<<<<<<<<<<
- *
- * cdef class IndelCaller( IndelCallerBase ):
+ /* "csamtools.pyx":3082
+ * property is_head:
+ * def __get__(self):
+ * return self._is_head # <<<<<<<<<<<<<<
+ * property is_tail:
+ * def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_call));
- __pyx_r = ((PyObject *)__pyx_v_call);
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IndelCallerBase._call");
+ __Pyx_AddTraceback("csamtools.PileupRead.is_head.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_DECREF((PyObject *)__pyx_v_call);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3300
- * '''
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * IteratorColumn iterator_column,
- * **kwargs ):
- */
-
-static int __pyx_pf_9csamtools_11IndelCaller___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_11IndelCaller___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_iterator_column = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__iterator_column,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 3300);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__iterator_column);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3300; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)PyTuple_GET_ITEM(__pyx_args, 0));
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3300; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IndelCaller.__cinit__");
- __Pyx_RefNannyFinishContext();
- return -1;
- __pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_iterator_column), __pyx_ptype_9csamtools_IteratorColumn, 1, "iterator_column", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.IndelCaller.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3306
- * pass
- *
- * def call(self, reference, int pos ): # <<<<<<<<<<<<<<
- * """call a snp on chromosome *reference*
- * and position *pos*.
+/* "csamtools.pyx":3084
+ * return self._is_head
+ * property is_tail:
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._is_tail
+ * property level:
*/
-static PyObject *__pyx_pf_9csamtools_11IndelCaller_call(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_11IndelCaller_call[] = "IndelCaller.call(self, reference, int pos)\ncall a snp on chromosome *reference*\n and position *pos*.\n\n returns a :class:`SNPCall` object or None, if no indel call could be made.\n ";
-static PyObject *__pyx_pf_9csamtools_11IndelCaller_call(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_reference = 0;
- int __pyx_v_pos;
- int __pyx_v_tid;
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- int __pyx_t_6;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__pos,0};
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("call");
- __Pyx_TraceCall("call", __pyx_f[0], 3306);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("call", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "call") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_reference = values[0];
- __pyx_v_pos = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_pos == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_reference = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_pos = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_pos == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- goto __pyx_L4_argument_unpacking_done;
- __pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("call", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3306; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IndelCaller.call");
- __Pyx_RefNannyFinishContext();
- return NULL;
- __pyx_L4_argument_unpacking_done:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3313
- * """
- *
- * cdef int tid = self.iter.samfile.gettid( reference ) # <<<<<<<<<<<<<<
- *
- * self.iter.reset( tid, pos, pos + 1 )
- */
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter->samfile), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3313; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3313; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_reference);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
- __Pyx_GIVEREF(__pyx_v_reference);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3313; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3313; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_tid = __pyx_t_4;
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3084);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3315
- * cdef int tid = self.iter.samfile.gettid( reference )
- *
- * self.iter.reset( tid, pos, pos + 1 ) # <<<<<<<<<<<<<<
- *
- * while 1:
+ /* "csamtools.pyx":3085
+ * property is_tail:
+ * def __get__(self):
+ * return self._is_tail # <<<<<<<<<<<<<<
+ * property level:
+ * def __get__(self):
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyInt_FromLong((__pyx_v_pos + 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->reset(((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter, __pyx_t_3, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3317
- * self.iter.reset( tid, pos, pos + 1 )
- *
- * while 1: # <<<<<<<<<<<<<<
- * self.iter.cnext()
- *
- */
- while (1) {
- if (!1) break;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3318
- *
- * while 1:
- * self.iter.cnext() # <<<<<<<<<<<<<<
- *
- * if self.iter.n_plp < 0:
- */
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3320
- * self.iter.cnext()
- *
- * if self.iter.n_plp < 0: # <<<<<<<<<<<<<<
- * raise ValueError("error during iteration" )
- *
- */
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter->n_plp < 0);
- if (__pyx_t_6) {
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3321
- *
- * if self.iter.n_plp < 0:
- * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
- *
- * if self.iter.plp == NULL:
- */
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_59));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_kp_s_59));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_59));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
- }
- __pyx_L8:;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.PileupRead.is_tail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3323
- * raise ValueError("error during iteration" )
- *
- * if self.iter.plp == NULL: # <<<<<<<<<<<<<<
- * raise ValueError( "no reads in region - no call" )
- *
- */
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter->plp == NULL);
- if (__pyx_t_6) {
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_10PileupRead_5level___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3324
- *
- * if self.iter.plp == NULL:
- * raise ValueError( "no reads in region - no call" ) # <<<<<<<<<<<<<<
+/* "csamtools.pyx":3087
+ * return self._is_tail
+ * property level:
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._level
*
- * if self.iter.pos == pos: break
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_109));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_109));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_109));
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
- }
- __pyx_L9:;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3326
- * raise ValueError( "no reads in region - no call" )
- *
- * if self.iter.pos == pos: break # <<<<<<<<<<<<<<
- *
- * return self._call()
- */
- __pyx_t_6 = (((struct __pyx_obj_9csamtools_IndelCaller *)__pyx_v_self)->__pyx_base.iter->pos == __pyx_v_pos);
- if (__pyx_t_6) {
- goto __pyx_L7_break;
- goto __pyx_L10;
- }
- __pyx_L10:;
- }
- __pyx_L7_break:;
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3087);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3328
- * if self.iter.pos == pos: break
- *
- * return self._call() # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3088
+ * property level:
+ * def __get__(self):
+ * return self._level # <<<<<<<<<<<<<<
*
- * cdef class IteratorIndelCalls( IndelCallerBase ):
+ * class Outs:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___call); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IndelCaller.call");
+ __Pyx_AddTraceback("csamtools.PileupRead.level.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3344
- * """
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * IteratorColumn iterator_column,
- * **kwargs ):
- */
-
-static int __pyx_pf_9csamtools_18IteratorIndelCalls___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_18IteratorIndelCalls___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_iterator_column = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__iterator_column,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 3344);
- __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
- PyObject* values[1] = {0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__iterator_column);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)values[0]);
- } else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_iterator_column = ((struct __pyx_obj_9csamtools_IteratorColumn *)PyTuple_GET_ITEM(__pyx_args, 0));
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_9csamtools_4Outs_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs___init__)};
+static PyObject *__pyx_pw_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_self = 0;
+ PyObject *__pyx_v_id = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ {
+ PyObject* values[2] = {0,0};
+ values[1] = ((PyObject *)((PyObject *)__pyx_int_1));
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__id);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_self = values[0];
+ __pyx_v_id = values[1];
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_AddTraceback("csamtools.IteratorIndelCalls.__cinit__");
+ __Pyx_AddTraceback("csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
- return -1;
+ return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_iterator_column), __pyx_ptype_9csamtools_IteratorColumn, 1, "iterator_column", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.IteratorIndelCalls.__cinit__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_kwargs);
- __Pyx_TraceReturn(Py_None);
+ __pyx_r = __pyx_pf_9csamtools_4Outs___init__(__pyx_self, __pyx_v_self, __pyx_v_id);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3350
- *
- *
- * def __iter__(self): # <<<<<<<<<<<<<<
- * return self
- *
+/* "csamtools.pyx":3092
+ * class Outs:
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1): # <<<<<<<<<<<<<<
+ * self.streams = []
+ * self.id = id
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorIndelCalls___iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_18IteratorIndelCalls___iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 3350);
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3092);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3351
+ /* "csamtools.pyx":3093
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1):
+ * self.streams = [] # <<<<<<<<<<<<<<
+ * self.id = id
*
- * def __iter__(self):
- * return self # <<<<<<<<<<<<<<
+ */
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__streams, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":3094
+ * def __init__(self, id = 1):
+ * self.streams = []
+ * self.id = id # <<<<<<<<<<<<<<
*
- * def __next__(self):
+ * def setdevice(self, filename):
*/
- __Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
- goto __pyx_L0;
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__id, __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3353
- * return self
- *
- * def __next__(self): # <<<<<<<<<<<<<<
- * """python version of next().
- * """
- */
-
-static PyObject *__pyx_pf_9csamtools_18IteratorIndelCalls___next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorIndelCalls___next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__;
-static PyObject *__pyx_pf_9csamtools_18IteratorIndelCalls___next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 3353);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3358
- *
- * # the following code was adapted from bam_plcmd.c:pileup_func()
- * self.iter.cnext() # <<<<<<<<<<<<<<
- *
- * if self.iter.n_plp < 0:
- */
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumn *)((struct __pyx_obj_9csamtools_IteratorIndelCalls *)__pyx_v_self)->__pyx_base.iter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorIndelCalls *)__pyx_v_self)->__pyx_base.iter);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3360
- * self.iter.cnext()
- *
- * if self.iter.n_plp < 0: # <<<<<<<<<<<<<<
- * raise ValueError("error during iteration" )
- *
- */
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorIndelCalls *)__pyx_v_self)->__pyx_base.iter->n_plp < 0);
- if (__pyx_t_1) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3361
- *
- * if self.iter.n_plp < 0:
- * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
- *
- * if self.iter.plp == NULL:
- */
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_59));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_59));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_59));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_2setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_3setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pw_9csamtools_4Outs_3setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_2setdevice)};
+static PyObject *__pyx_pw_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_self = 0;
+ PyObject *__pyx_v_filename = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("setdevice (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ {
+ PyObject* values[2] = {0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ }
+ __pyx_v_self = values[0];
+ __pyx_v_filename = values[1];
}
- __pyx_L5:;
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_4Outs_2setdevice(__pyx_self, __pyx_v_self, __pyx_v_filename);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3363
- * raise ValueError("error during iteration" )
- *
- * if self.iter.plp == NULL: # <<<<<<<<<<<<<<
- * raise StopIteration
+/* "csamtools.pyx":3096
+ * self.id = id
*
+ * def setdevice(self, filename): # <<<<<<<<<<<<<<
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorIndelCalls *)__pyx_v_self)->__pyx_base.iter->plp == NULL);
- if (__pyx_t_1) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3364
- *
- * if self.iter.plp == NULL:
- * raise StopIteration # <<<<<<<<<<<<<<
+static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setdevice", 0);
+ __Pyx_TraceCall("setdevice", __pyx_f[0], 3096);
+
+ /* "csamtools.pyx":3098
+ * def setdevice(self, filename):
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY) # <<<<<<<<<<<<<<
+ * self.setfd(fd)
*
- * return self._call()
*/
- __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
- }
- __pyx_L6:;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
+ __Pyx_GIVEREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_v_fd = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3366
- * raise StopIteration
- *
- * return self._call() # <<<<<<<<<<<<<<
- *
+ /* "csamtools.pyx":3099
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
+ * self.setfd(fd) # <<<<<<<<<<<<<<
*
+ * def setfile(self, filename):
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___call); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_fd);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fd);
+ __Pyx_GIVEREF(__pyx_v_fd);
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IteratorIndelCalls.__next__");
+ __Pyx_AddTraceback("csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_fd);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3386
- * cdef int owns_samfile
- *
- * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- *
- */
-
-static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- int __pyx_v_reopen;
- PyObject *__pyx_v_mode;
- PyObject *__pyx_v_store;
- int __pyx_r;
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- char *__pyx_t_3;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 3386);
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_4setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_5setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pw_9csamtools_4Outs_5setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_4setfile)};
+static PyObject *__pyx_pw_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_self = 0;
+ PyObject *__pyx_v_filename = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("setfile (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ {
PyObject* values[2] = {0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
- if (value) { values[1] = value; kw_args--; }
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
}
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3386; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- if (values[1]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3386; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
+ goto __pyx_L5_argtuple_error;
} else {
- __pyx_v_reopen = ((int)1);
- }
- } else {
- __pyx_v_reopen = ((int)1);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 2: __pyx_v_reopen = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3386; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- case 1: __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 0));
- break;
- default: goto __pyx_L5_argtuple_error;
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
}
+ __pyx_v_self = values[0];
+ __pyx_v_filename = values[1];
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3386; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IndexedReads.__init__");
+ __Pyx_AddTraceback("csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
- return -1;
+ return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_v_mode = Py_None; __Pyx_INCREF(Py_None);
- __pyx_v_store = Py_None; __Pyx_INCREF(Py_None);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3387
- *
- * def __init__(self, Samfile samfile, int reopen = True ):
- * self.samfile = samfile # <<<<<<<<<<<<<<
- *
- * if samfile.isbam: mode = "rb"
- */
- __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile = __pyx_v_samfile;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3389
- * self.samfile = samfile
- *
- * if samfile.isbam: mode = "rb" # <<<<<<<<<<<<<<
- * else: mode = "r"
- *
- */
- if (__pyx_v_samfile->isbam) {
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__rb);
- goto __pyx_L6;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3390
- *
- * if samfile.isbam: mode = "rb"
- * else: mode = "r" # <<<<<<<<<<<<<<
- *
- * # reopen the file - note that this makes the iterator
- */
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- __Pyx_DECREF(__pyx_v_mode);
- __pyx_v_mode = ((PyObject *)__pyx_n_s__r);
- }
- __pyx_L6:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3394
- * # reopen the file - note that this makes the iterator
- * # slow and causes pileup to slow down significantly.
- * if reopen: # <<<<<<<<<<<<<<
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
- */
- if (__pyx_v_reopen) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3395
- * # slow and causes pileup to slow down significantly.
- * if reopen:
- * store = StderrStore() # <<<<<<<<<<<<<<
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_v_store);
- __pyx_v_store = __pyx_t_2;
- __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3396
- * if reopen:
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
- * store.release()
- * assert self.fp != NULL
- */
- __pyx_t_3 = PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3397
- * store = StderrStore()
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release() # <<<<<<<<<<<<<<
- * assert self.fp != NULL
- * self.owns_samfile = True
- */
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3398
- * self.fp = samopen( samfile._filename, mode, NULL )
- * store.release()
- * assert self.fp != NULL # <<<<<<<<<<<<<<
- * self.owns_samfile = True
- * else:
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp != NULL))) {
- PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3399
- * store.release()
- * assert self.fp != NULL
- * self.owns_samfile = True # <<<<<<<<<<<<<<
- * else:
- * self.fp = samfile.samfile
- */
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L7;
- }
- /*else*/ {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3401
- * self.owns_samfile = True
- * else:
- * self.fp = samfile.samfile # <<<<<<<<<<<<<<
- * self.owns_samfile = False
- *
- */
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3402
- * else:
- * self.fp = samfile.samfile
- * self.owns_samfile = False # <<<<<<<<<<<<<<
- *
- * assert samfile.isbam, "can only IndexReads on bam files"
- */
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 0;
- }
- __pyx_L7:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3404
- * self.owns_samfile = False
- *
- * assert samfile.isbam, "can only IndexReads on bam files" # <<<<<<<<<<<<<<
- *
- * def build( self ):
- */
- #ifndef PYREX_WITHOUT_ASSERTIONS
- if (unlikely(!__pyx_v_samfile->isbam)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_112));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #endif
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IndexedReads.__init__");
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_DECREF(__pyx_v_mode);
- __Pyx_DECREF(__pyx_v_store);
- __Pyx_TraceReturn(Py_None);
+ __pyx_r = __pyx_pf_9csamtools_4Outs_4setfile(__pyx_self, __pyx_v_self, __pyx_v_filename);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3406
- * assert samfile.isbam, "can only IndexReads on bam files"
- *
- * def build( self ): # <<<<<<<<<<<<<<
- * '''build index.'''
+/* "csamtools.pyx":3101
+ * self.setfd(fd)
*
+ * def setfile(self, filename): # <<<<<<<<<<<<<<
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
*/
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_12IndexedReads_build[] = "IndexedReads.build(self)\nbuild index.";
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- int __pyx_v_ret;
- bam1_t *__pyx_v_b;
- uint64_t __pyx_v_pos;
- char *__pyx_v_qname;
+static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_v_fd = NULL;
PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("build");
- __Pyx_TraceCall("build", __pyx_f[0], 3406);
+ __Pyx_RefNannySetupContext("setfile", 0);
+ __Pyx_TraceCall("setfile", __pyx_f[0], 3101);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3409
- * '''build index.'''
- *
- * self.index = collections.defaultdict( list ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3103
+ * def setfile(self, filename):
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660); # <<<<<<<<<<<<<<
+ * self.setfd(fd)
*
- * # this method will start indexing from the current file position
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__collections); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)((PyObject*)&PyList_Type)));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)&PyList_Type)));
- __Pyx_GIVEREF(((PyObject *)((PyObject*)&PyList_Type)));
- __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_GIVEREF(__pyx_t_3);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
- __Pyx_DECREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_CREAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Or(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_INCREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_filename);
+ __Pyx_GIVEREF(__pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_int_0660);
+ PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_int_0660);
+ __Pyx_GIVEREF(__pyx_int_0660);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_v_fd = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3413
- * # this method will start indexing from the current file position
- * # if you decide
- * cdef int ret = 1 # <<<<<<<<<<<<<<
- * cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) )
+ /* "csamtools.pyx":3104
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+ * self.setfd(fd) # <<<<<<<<<<<<<<
*
+ * def setfd(self, fd):
*/
- __pyx_v_ret = 1;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_INCREF(__pyx_v_fd);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_fd);
+ __Pyx_GIVEREF(__pyx_v_fd);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3414
- * # if you decide
- * cdef int ret = 1
- * cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
- *
- * cdef uint64_t pos
- */
- __pyx_v_b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_fd);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3418
- * cdef uint64_t pos
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_6setfd[] = "Outs.setfd(self, fd)";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_7setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pw_9csamtools_4Outs_7setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_6setfd)};
+static PyObject *__pyx_pw_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_self = 0;
+ PyObject *__pyx_v_fd = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("setfd (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ {
+ PyObject* values[2] = {0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fd);
+ if (likely(values[1])) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ }
+ __pyx_v_self = values[0];
+ __pyx_v_fd = values[1];
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools_4Outs_6setfd(__pyx_self, __pyx_v_self, __pyx_v_fd);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3106
+ * self.setfd(fd)
*
- * while ret > 0: # <<<<<<<<<<<<<<
- * pos = bam_tell( self.fp.x.bam )
- * ret = samread( self.fp, b)
+ * def setfd(self, fd): # <<<<<<<<<<<<<<
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
*/
- while (1) {
- __pyx_t_4 = (__pyx_v_ret > 0);
- if (!__pyx_t_4) break;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3419
+static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd) {
+ PyObject *__pyx_v_ofd = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfd", 0);
+ __Pyx_TraceCall("setfd", __pyx_f[0], 3106);
+
+ /* "csamtools.pyx":3107
*
- * while ret > 0:
- * pos = bam_tell( self.fp.x.bam ) # <<<<<<<<<<<<<<
- * ret = samread( self.fp, b)
- * if ret > 0:
+ * def setfd(self, fd):
+ * ofd = os.dup(self.id) # Save old stream on new unit. # <<<<<<<<<<<<<<
+ * self.streams.append(ofd)
+ * sys.stdout.flush() # Buffered data goes to old stream.
*/
- __pyx_v_pos = bam_tell(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp->x.bam);
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_v_ofd = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3420
- * while ret > 0:
- * pos = bam_tell( self.fp.x.bam )
- * ret = samread( self.fp, b) # <<<<<<<<<<<<<<
- * if ret > 0:
- * qname = bam1_qname( b )
+ /* "csamtools.pyx":3108
+ * def setfd(self, fd):
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd) # <<<<<<<<<<<<<<
+ * sys.stdout.flush() # Buffered data goes to old stream.
+ * sys.stderr.flush() # Buffered data goes to old stream.
*/
- __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp, __pyx_v_b);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = __Pyx_PyObject_Append(__pyx_t_1, __pyx_v_ofd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3421
- * pos = bam_tell( self.fp.x.bam )
- * ret = samread( self.fp, b)
- * if ret > 0: # <<<<<<<<<<<<<<
- * qname = bam1_qname( b )
- * self.index[qname].append( pos )
+ /* "csamtools.pyx":3109
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
+ * sys.stdout.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
+ * sys.stderr.flush() # Buffered data goes to old stream.
+ * os.dup2(fd, self.id) # Open unit 1 on new stream.
*/
- __pyx_t_4 = (__pyx_v_ret > 0);
- if (__pyx_t_4) {
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3422
- * ret = samread( self.fp, b)
- * if ret > 0:
- * qname = bam1_qname( b ) # <<<<<<<<<<<<<<
- * self.index[qname].append( pos )
- *
+ /* "csamtools.pyx":3110
+ * self.streams.append(ofd)
+ * sys.stdout.flush() # Buffered data goes to old stream.
+ * sys.stderr.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
+ * os.dup2(fd, self.id) # Open unit 1 on new stream.
+ * os.close(fd) # Close other unit (look out, caller.)
*/
- __pyx_v_qname = bam1_qname(__pyx_v_b);
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stderr); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3423
- * if ret > 0:
- * qname = bam1_qname( b )
- * self.index[qname].append( pos ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3111
+ * sys.stdout.flush() # Buffered data goes to old stream.
+ * sys.stderr.flush() # Buffered data goes to old stream.
+ * os.dup2(fd, self.id) # Open unit 1 on new stream. # <<<<<<<<<<<<<<
+ * os.close(fd) # Close other unit (look out, caller.)
*
- * bam_destroy1( b )
*/
- __pyx_t_3 = PyBytes_FromString(__pyx_v_qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_1 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, ((PyObject *)__pyx_t_3)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_to_py_uint64_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_PyObject_Append(__pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L7;
- }
- __pyx_L7:;
- }
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__dup2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_fd);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_fd);
+ __Pyx_GIVEREF(__pyx_v_fd);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3425
- * self.index[qname].append( pos )
- *
- * bam_destroy1( b ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3112
+ * sys.stderr.flush() # Buffered data goes to old stream.
+ * os.dup2(fd, self.id) # Open unit 1 on new stream.
+ * os.close(fd) # Close other unit (look out, caller.) # <<<<<<<<<<<<<<
*
- * def find( self, qname ):
+ * def restore(self):
*/
- bam_destroy1(__pyx_v_b);
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_v_fd);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fd);
+ __Pyx_GIVEREF(__pyx_v_fd);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IndexedReads.build");
+ __Pyx_AddTraceback("csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_ofd);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3427
- * bam_destroy1( b )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_8restore[] = "Outs.restore(self)\nrestore previous output stream";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_9restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pw_9csamtools_4Outs_9restore, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_8restore)};
+static PyObject *__pyx_pw_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("restore (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ __pyx_r = __pyx_pf_9csamtools_4Outs_8restore(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3114
+ * os.close(fd) # Close other unit (look out, caller.)
*
- * def find( self, qname ): # <<<<<<<<<<<<<<
- * if qname in self.index:
- * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
+ * def restore(self): # <<<<<<<<<<<<<<
+ * '''restore previous output stream'''
+ * if self.streams:
*/
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static char __pyx_doc_9csamtools_12IndexedReads_find[] = "IndexedReads.find(self, qname)";
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("find");
- __Pyx_TraceCall("find", __pyx_f[0], 3427);
+ __Pyx_RefNannySetupContext("restore", 0);
+ __Pyx_TraceCall("restore", __pyx_f[0], 3114);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3428
- *
- * def find( self, qname ):
- * if qname in self.index: # <<<<<<<<<<<<<<
- * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
- * else:
- */
- __pyx_t_1 = ((PySequence_Contains(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
+ /* "csamtools.pyx":3116
+ * def restore(self):
+ * '''restore previous output stream'''
+ * if self.streams: # <<<<<<<<<<<<<<
+ * # the following was not sufficient, hence flush both stderr and stdout
+ * # os.fsync( self.id )
+ */
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3429
- * def find( self, qname ):
- * if qname in self.index:
- * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False ) # <<<<<<<<<<<<<<
- * else:
- * raise KeyError( "read %s not found" % qname )
+ /* "csamtools.pyx":3119
+ * # the following was not sufficient, hence flush both stderr and stdout
+ * # os.fsync( self.id )
+ * sys.stdout.flush() # <<<<<<<<<<<<<<
+ * sys.stderr.flush()
+ * os.dup2(self.streams[-1], self.id)
*/
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stdout); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), __pyx_t_3, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_r = __pyx_t_4;
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+
+ /* "csamtools.pyx":3120
+ * # os.fsync( self.id )
+ * sys.stdout.flush()
+ * sys.stderr.flush() # <<<<<<<<<<<<<<
+ * os.dup2(self.streams[-1], self.id)
+ * os.close(self.streams[-1])
+ */
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stderr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":3121
+ * sys.stdout.flush()
+ * sys.stderr.flush()
+ * os.dup2(self.streams[-1], self.id) # <<<<<<<<<<<<<<
+ * os.close(self.streams[-1])
+ * del self.streams[-1]
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
__pyx_t_4 = 0;
- goto __pyx_L0;
- goto __pyx_L5;
- }
- /*else*/ {
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3431
- * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
- * else:
- * raise KeyError( "read %s not found" % qname ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3122
+ * sys.stderr.flush()
+ * os.dup2(self.streams[-1], self.id)
+ * os.close(self.streams[-1]) # <<<<<<<<<<<<<<
+ * del self.streams[-1]
*
- * def __dealloc__(self):
*/
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_113), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_KeyError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+
+ /* "csamtools.pyx":3123
+ * os.dup2(self.streams[-1], self.id)
+ * os.close(self.streams[-1])
+ * del self.streams[-1] # <<<<<<<<<<<<<<
+ *
+ * def _samtools_dispatch( method,
+ */
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (__Pyx_DelItemInt(__pyx_t_3, -1, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.IndexedReads.find");
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("csamtools.Outs.restore", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3433
- * raise KeyError( "read %s not found" % qname )
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout to capture it \n from samtools. If for some reason stdout disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n\n .. note::\n This method captures stdout and stderr using temporary files,\n which are then read into memory in their entirety. This method\n is slow and might cause large memory overhead.\n\n See http://bytes.com/topic/c/answers/487231-how-capture-stdout-temporarily\n on the topic of redirecting stderr/stdout.\n ";
+static PyMethodDef __pyx_mdef_9csamtools_1_samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pw_9csamtools_1_samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools__samtools_dispatch)};
+static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_method = 0;
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_catch_stdout = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_samtools_dispatch (wrapper)", 0);
+ __pyx_self = __pyx_self;
+ {
+ PyObject* values[3] = {0,0,0};
+
+ /* "csamtools.pyx":3126
*
- * def __dealloc__(self): # <<<<<<<<<<<<<<
- * if self.owns_samfile: samclose( self.fp )
+ * def _samtools_dispatch( method,
+ * args = (), # <<<<<<<<<<<<<<
+ * catch_stdout = True ):
+ * '''call ``method`` in samtools providing arguments in args.
+ */
+ values[1] = ((PyObject *)__pyx_empty_tuple);
+ values[2] = __pyx_k_176;
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__args);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ case 2:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__catch_stdout);
+ if (value) { values[2] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_method = values[0];
+ __pyx_v_args = values[1];
+ __pyx_v_catch_stdout = values[2];
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return NULL;
+ __pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_9csamtools__samtools_dispatch(__pyx_self, __pyx_v_method, __pyx_v_args, __pyx_v_catch_stdout);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3125
+ * del self.streams[-1]
*
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
+ * args = (),
+ * catch_stdout = True ):
*/
-static void __pyx_pf_9csamtools_12IndexedReads___dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_12IndexedReads___dealloc__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout) {
+ PyObject *__pyx_v_stderr_h = NULL;
+ PyObject *__pyx_v_stderr_f = NULL;
+ PyObject *__pyx_v_stdout_h = NULL;
+ PyObject *__pyx_v_stdout_f = NULL;
+ PyObject *__pyx_v_stdout_save = NULL;
+ char **__pyx_v_cargs;
+ int __pyx_v_i;
+ int __pyx_v_n;
+ int __pyx_v_retval;
+ PyObject *__pyx_v_inf = NULL;
+ PyObject *__pyx_v_out_stdout = NULL;
+ PyObject *__pyx_v_out_stderr = NULL;
+ PyObject *__pyx_v_a = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *(*__pyx_t_7)(PyObject *);
+ int __pyx_t_8;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ PyObject *(*__pyx_t_13)(PyObject *);
+ char *__pyx_t_14;
+ PyObject *__pyx_t_15 = NULL;
+ PyObject *__pyx_t_16 = NULL;
+ PyObject *__pyx_t_17 = NULL;
+ PyObject *__pyx_t_18 = NULL;
+ PyObject *__pyx_t_19 = NULL;
+ PyObject *__pyx_t_20 = NULL;
+ PyObject *__pyx_t_21 = NULL;
+ PyObject *__pyx_t_22 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3433);
+ __Pyx_RefNannySetupContext("_samtools_dispatch", 0);
+ __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125);
+ __Pyx_INCREF(__pyx_v_method);
+ __Pyx_INCREF(__pyx_v_args);
+ __Pyx_INCREF(__pyx_v_catch_stdout);
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3434
- *
- * def __dealloc__(self):
- * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3151
*
- * __all__ = ["Samfile",
+ * # some special cases
+ * if method == "index": # <<<<<<<<<<<<<<
+ * if not os.path.exists( args[0] ):
+ * raise IOError( "No such file or directory: '%s'" % args[0] )
*/
- if (((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp);
- goto __pyx_L5;
- }
- __pyx_L5:;
-
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
-}
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_method, ((PyObject *)__pyx_n_s__index), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
-static PyObject *__pyx_tp_new_9csamtools_AlignedRead(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- return o;
-}
+ /* "csamtools.pyx":3152
+ * # some special cases
+ * if method == "index":
+ * if not os.path.exists( args[0] ): # <<<<<<<<<<<<<<
+ * raise IOError( "No such file or directory: '%s'" % args[0] )
+ *
+ */
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_5 = (!__pyx_t_1);
+ if (__pyx_t_5) {
-static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_11AlignedRead___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
+ /* "csamtools.pyx":3153
+ * if method == "index":
+ * if not os.path.exists( args[0] ):
+ * raise IOError( "No such file or directory: '%s'" % args[0] ) # <<<<<<<<<<<<<<
+ *
+ * # redirect stderr and stdout to file
+ */
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_177), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_Raise(__pyx_t_4, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+ goto __pyx_L3;
}
- (*Py_TYPE(o)->tp_free)(o);
-}
+ __pyx_L3:;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o);
-}
-
-static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5qname___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o);
-}
-
-static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5cigar___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+ /* "csamtools.pyx":3156
+ *
+ * # redirect stderr and stdout to file
+ * stderr_h, stderr_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
+ * pysam_set_stderr( stderr_h )
+ *
+ */
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
+ PyObject* sequence = __pyx_t_4;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_3 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
+ index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_3);
+ index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L6_unpacking_done;
+ __pyx_L5_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L6_unpacking_done:;
}
-}
+ __pyx_v_stderr_h = __pyx_t_3;
+ __pyx_t_3 = 0;
+ __pyx_v_stderr_f = __pyx_t_2;
+ __pyx_t_2 = 0;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o);
-}
+ /* "csamtools.pyx":3157
+ * # redirect stderr and stdout to file
+ * stderr_h, stderr_f = tempfile.mkstemp()
+ * pysam_set_stderr( stderr_h ) # <<<<<<<<<<<<<<
+ *
+ * if catch_stdout:
+ */
+ __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_v_stderr_h); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ pysam_set_stderr(__pyx_t_8);
-static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3seq___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3159
+ * pysam_set_stderr( stderr_h )
+ *
+ * if catch_stdout: # <<<<<<<<<<<<<<
+ * stdout_h, stdout_f = tempfile.mkstemp()
+ * try:
+ */
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o);
-}
+ /* "csamtools.pyx":3160
+ *
+ * if catch_stdout:
+ * stdout_h, stdout_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
+ * try:
+ * stdout_save = Outs( sys.stdout.fileno() )
+ */
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
+ PyObject* sequence = __pyx_t_4;
+ if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
+ } else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_3 = PyList_GET_ITEM(sequence, 1);
+ }
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ } else {
+ Py_ssize_t index = -1;
+ __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
+ index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_3);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L9_unpacking_done:;
+ }
+ __pyx_v_stdout_h = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __pyx_v_stdout_f = __pyx_t_3;
+ __pyx_t_3 = 0;
-static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4qual___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3161
+ * if catch_stdout:
+ * stdout_h, stdout_f = tempfile.mkstemp()
+ * try: # <<<<<<<<<<<<<<
+ * stdout_save = Outs( sys.stdout.fileno() )
+ * stdout_save.setfd( stdout_h )
+ */
+ {
+ __Pyx_ExceptionSave(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11);
+ __Pyx_XGOTREF(__pyx_t_9);
+ __Pyx_XGOTREF(__pyx_t_10);
+ __Pyx_XGOTREF(__pyx_t_11);
+ /*try:*/ {
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o);
-}
+ /* "csamtools.pyx":3162
+ * stdout_h, stdout_f = tempfile.mkstemp()
+ * try:
+ * stdout_save = Outs( sys.stdout.fileno() ) # <<<<<<<<<<<<<<
+ * stdout_save.setfd( stdout_h )
+ * except AttributeError:
+ */
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_v_stdout_save = __pyx_t_2;
+ __pyx_t_2 = 0;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o);
-}
+ /* "csamtools.pyx":3163
+ * try:
+ * stdout_save = Outs( sys.stdout.fileno() )
+ * stdout_save.setfd( stdout_h ) # <<<<<<<<<<<<<<
+ * except AttributeError:
+ * # stdout has already been redirected
+ */
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_v_stdout_h);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_h);
+ __Pyx_GIVEREF(__pyx_v_stdout_h);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L17_try_end;
+ __pyx_L10_error:;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o);
-}
+ /* "csamtools.pyx":3164
+ * stdout_save = Outs( sys.stdout.fileno() )
+ * stdout_save.setfd( stdout_h )
+ * except AttributeError: # <<<<<<<<<<<<<<
+ * # stdout has already been redirected
+ * catch_stdout = False
+ */
+ __pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_AttributeError);
+ if (__pyx_t_8) {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_2);
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o);
-}
+ /* "csamtools.pyx":3166
+ * except AttributeError:
+ * # stdout has already been redirected
+ * catch_stdout = False # <<<<<<<<<<<<<<
+ *
+ * # patch for `samtools view`
+ */
+ __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3166; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_v_catch_stdout);
+ __pyx_v_catch_stdout = __pyx_t_6;
+ __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L11_exception_handled;
+ }
+ __pyx_L12_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
+ goto __pyx_L1_error;
+ __pyx_L11_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
+ __pyx_L17_try_end:;
+ }
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o);
-}
+ /* "csamtools.pyx":3171
+ * # samtools `view` closes stdout, from which I can not
+ * # recover. Thus redirect output to file with -o option.
+ * if method == "view": # <<<<<<<<<<<<<<
+ * if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
+ * args = ( "-o", stdout_f ) + args
+ */
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_method, ((PyObject *)__pyx_n_s__view), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o);
-}
+ /* "csamtools.pyx":3172
+ * # recover. Thus redirect output to file with -o option.
+ * if method == "view":
+ * if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
+ * args = ( "-o", stdout_f ) + args
+ *
+ */
+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_args, ((PyObject *)__pyx_kp_s_178)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_180), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L21;
+ }
+ __pyx_L21:;
-static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4tags___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+ /* "csamtools.pyx":3173
+ * if method == "view":
+ * if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
+ * args = ( "-o", stdout_f ) + args # <<<<<<<<<<<<<<
+ *
+ * # do the function call to samtools
+ */
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_178));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_178));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_178));
+ __Pyx_INCREF(__pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_stdout_f);
+ __Pyx_GIVEREF(__pyx_v_stdout_f);
+ __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_2), __pyx_v_args); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_v_args);
+ __pyx_v_args = __pyx_t_3;
+ __pyx_t_3 = 0;
+ goto __pyx_L20;
+ }
+ __pyx_L20:;
+ goto __pyx_L7;
}
-}
-
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
-}
+ __pyx_L7:;
-static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4flag___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3179
+ * cdef int i, n, retval
+ *
+ * n = len(args) # <<<<<<<<<<<<<<
+ * method = _force_cmdline_bytes(method)
+ * args = [ _force_cmdline_bytes(a) for a in args ]
+ */
+ __pyx_t_12 = PyObject_Length(__pyx_v_args); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_n = __pyx_t_12;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
-}
+ /* "csamtools.pyx":3180
+ *
+ * n = len(args)
+ * method = _force_cmdline_bytes(method) # <<<<<<<<<<<<<<
+ * args = [ _force_cmdline_bytes(a) for a in args ]
+ *
+ */
+ __pyx_t_3 = ((PyObject *)__pyx_f_9csamtools__force_cmdline_bytes(__pyx_v_method)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_v_method);
+ __pyx_v_method = __pyx_t_3;
+ __pyx_t_3 = 0;
-static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5rname___set__(o, v);
+ /* "csamtools.pyx":3181
+ * n = len(args)
+ * method = _force_cmdline_bytes(method)
+ * args = [ _force_cmdline_bytes(a) for a in args ] # <<<<<<<<<<<<<<
+ *
+ * # allocate two more for first (dummy) argument (contains command)
+ */
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (PyList_CheckExact(__pyx_v_args) || PyTuple_CheckExact(__pyx_v_args)) {
+ __pyx_t_2 = __pyx_v_args; __Pyx_INCREF(__pyx_t_2); __pyx_t_12 = 0;
+ __pyx_t_13 = NULL;
+ } else {
+ __pyx_t_12 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_13 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+ for (;;) {
+ if (!__pyx_t_13 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
+ } else if (!__pyx_t_13 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
+ } else {
+ __pyx_t_4 = __pyx_t_13(__pyx_t_2);
+ if (unlikely(!__pyx_t_4)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_4);
+ }
+ __Pyx_XDECREF(__pyx_v_a);
+ __pyx_v_a = __pyx_t_4;
+ __pyx_t_4 = 0;
+ __pyx_t_4 = ((PyObject *)__pyx_f_9csamtools__force_cmdline_bytes(__pyx_v_a)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
-}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_3));
+ __Pyx_DECREF(__pyx_v_args);
+ __pyx_v_args = ((PyObject *)__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
-}
+ /* "csamtools.pyx":3184
+ *
+ * # allocate two more for first (dummy) argument (contains command)
+ * cargs = <char**>calloc( n+2, sizeof( char *) ) # <<<<<<<<<<<<<<
+ * cargs[0] = "samtools"
+ * cargs[1] = method
+ */
+ __pyx_v_cargs = ((char **)calloc((__pyx_v_n + 2), (sizeof(char *))));
-static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3tid___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3185
+ * # allocate two more for first (dummy) argument (contains command)
+ * cargs = <char**>calloc( n+2, sizeof( char *) )
+ * cargs[0] = "samtools" # <<<<<<<<<<<<<<
+ * cargs[1] = method
+ * for i from 0 <= i < n: cargs[i+2] = args[i]
+ */
+ (__pyx_v_cargs[0]) = __pyx_k__samtools;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
-}
+ /* "csamtools.pyx":3186
+ * cargs = <char**>calloc( n+2, sizeof( char *) )
+ * cargs[0] = "samtools"
+ * cargs[1] = method # <<<<<<<<<<<<<<
+ * for i from 0 <= i < n: cargs[i+2] = args[i]
+ *
+ */
+ __pyx_t_14 = PyBytes_AsString(__pyx_v_method); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_cargs[1]) = __pyx_t_14;
-static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3pos___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+ /* "csamtools.pyx":3187
+ * cargs[0] = "samtools"
+ * cargs[1] = method
+ * for i from 0 <= i < n: cargs[i+2] = args[i] # <<<<<<<<<<<<<<
+ *
+ * retval = pysam_dispatch(n+2, cargs)
+ */
+ __pyx_t_8 = __pyx_v_n;
+ for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_8; __pyx_v_i++) {
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_14 = PyBytes_AsString(__pyx_t_3); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ (__pyx_v_cargs[(__pyx_v_i + 2)]) = __pyx_t_14;
}
-}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
-}
+ /* "csamtools.pyx":3189
+ * for i from 0 <= i < n: cargs[i+2] = args[i]
+ *
+ * retval = pysam_dispatch(n+2, cargs) # <<<<<<<<<<<<<<
+ * free( cargs )
+ *
+ */
+ __pyx_v_retval = pysam_dispatch((__pyx_v_n + 2), __pyx_v_cargs);
-static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3bin___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3190
+ *
+ * retval = pysam_dispatch(n+2, cargs)
+ * free( cargs ) # <<<<<<<<<<<<<<
+ *
+ * # restore stdout/stderr. This will also flush, so
+ */
+ free(__pyx_v_cargs);
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
-}
+ /* "csamtools.pyx":3194
+ * # restore stdout/stderr. This will also flush, so
+ * # needs to be before reading back the file contents
+ * if catch_stdout: # <<<<<<<<<<<<<<
+ * stdout_save.restore()
+ * try:
+ */
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_5) {
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
-}
+ /* "csamtools.pyx":3195
+ * # needs to be before reading back the file contents
+ * if catch_stdout:
+ * stdout_save.restore() # <<<<<<<<<<<<<<
+ * try:
+ * with open( stdout_f, "r") as inf:
+ */
+ if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
-}
+ /* "csamtools.pyx":3196
+ * if catch_stdout:
+ * stdout_save.restore()
+ * try: # <<<<<<<<<<<<<<
+ * with open( stdout_f, "r") as inf:
+ * out_stdout = inf.readlines()
+ */
+ {
+ __Pyx_ExceptionSave(&__pyx_t_11, &__pyx_t_10, &__pyx_t_9);
+ __Pyx_XGOTREF(__pyx_t_11);
+ __Pyx_XGOTREF(__pyx_t_10);
+ __Pyx_XGOTREF(__pyx_t_9);
+ /*try:*/ {
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
-}
+ /* "csamtools.pyx":3197
+ * stdout_save.restore()
+ * try:
+ * with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError:
+ */
+ /*with:*/ {
+ if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;} }
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
+ __Pyx_GIVEREF(__pyx_v_stdout_f);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
+ __Pyx_XGOTREF(__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_17);
+ __Pyx_XGOTREF(__pyx_t_18);
+ /*try:*/ {
+ __Pyx_INCREF(__pyx_t_4);
+ __pyx_v_inf = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+
+ /* "csamtools.pyx":3198
+ * try:
+ * with open( stdout_f, "r") as inf:
+ * out_stdout = inf.readlines() # <<<<<<<<<<<<<<
+ * except UnicodeDecodeError:
+ * with open( stdout_f, "rb") as inf:
+ */
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_out_stdout = __pyx_t_3;
+ __pyx_t_3 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
+ __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
+ goto __pyx_L48_try_end;
+ __pyx_L41_error:;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+
+ /* "csamtools.pyx":3197
+ * stdout_save.restore()
+ * try:
+ * with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError:
+ */
+ /*except:*/ {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_INCREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __Pyx_GOTREF(__pyx_t_19);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __pyx_t_1 = (!__pyx_t_5);
+ if (__pyx_t_1) {
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __Pyx_ErrRestore(__pyx_t_3, __pyx_t_4, __pyx_t_2);
+ __pyx_t_3 = 0; __pyx_t_4 = 0; __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ goto __pyx_L52;
+ }
+ __pyx_L52:;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L42_exception_handled;
+ }
+ __pyx_L43_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
+ goto __pyx_L27_error;
+ __pyx_L42_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
+ __pyx_L48_try_end:;
+ }
+ }
+ /*finally:*/ {
+ if (__pyx_t_15) {
+ __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_181, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __Pyx_GOTREF(__pyx_t_18);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
+ __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ }
+ }
+ goto __pyx_L53;
+ __pyx_L35_error:;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L27_error;
+ __pyx_L53:;
+ }
+ }
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ goto __pyx_L34_try_end;
+ __pyx_L27_error:;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
-static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mapq___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3199
+ * with open( stdout_f, "r") as inf:
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError: # <<<<<<<<<<<<<<
+ * with open( stdout_f, "rb") as inf:
+ * # read binary output
+ */
+ __pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
+ if (__pyx_t_8) {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_3);
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
-}
+ /* "csamtools.pyx":3200
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError:
+ * with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
+ * # read binary output
+ * out_stdout = inf.read()
+ */
+ /*with:*/ {
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stdout_f);
+ __Pyx_GIVEREF(__pyx_v_stdout_f);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_21 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_18);
+ __Pyx_XGOTREF(__pyx_t_17);
+ __Pyx_XGOTREF(__pyx_t_16);
+ /*try:*/ {
+ __Pyx_INCREF(__pyx_t_21);
+ __Pyx_XDECREF(__pyx_v_inf);
+ __pyx_v_inf = __pyx_t_21;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+
+ /* "csamtools.pyx":3202
+ * with open( stdout_f, "rb") as inf:
+ * # read binary output
+ * out_stdout = inf.read() # <<<<<<<<<<<<<<
+ * os.remove( stdout_f )
+ * else:
+ */
+ __pyx_t_21 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_v_out_stdout);
+ __pyx_v_out_stdout = __pyx_t_20;
+ __pyx_t_20 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
+ __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ goto __pyx_L69_try_end;
+ __pyx_L62_error:;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+
+ /* "csamtools.pyx":3200
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError:
+ * with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
+ * # read binary output
+ * out_stdout = inf.read()
+ */
+ /*except:*/ {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_20, &__pyx_t_21, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_INCREF(__pyx_t_20);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_20);
+ __Pyx_GIVEREF(__pyx_t_20);
+ __Pyx_INCREF(__pyx_t_21);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_21);
+ __Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_INCREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __Pyx_GOTREF(__pyx_t_19);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __pyx_t_5 = (!__pyx_t_1);
+ if (__pyx_t_5) {
+ __Pyx_GIVEREF(__pyx_t_20);
+ __Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_ErrRestore(__pyx_t_20, __pyx_t_21, __pyx_t_6);
+ __pyx_t_20 = 0; __pyx_t_21 = 0; __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ goto __pyx_L73;
+ }
+ __pyx_L73:;
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L63_exception_handled;
+ }
+ __pyx_L64_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
+ goto __pyx_L29_except_error;
+ __pyx_L63_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
+ __pyx_L69_try_end:;
+ }
+ }
+ /*finally:*/ {
+ if (__pyx_t_15) {
+ __pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_182, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __Pyx_GOTREF(__pyx_t_16);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
+ __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ }
+ }
+ goto __pyx_L74;
+ __pyx_L56_error:;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L29_except_error;
+ __pyx_L74:;
+ }
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L28_exception_handled;
+ }
+ __pyx_L29_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
+ goto __pyx_L1_error;
+ __pyx_L28_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
+ __pyx_L34_try_end:;
+ }
-static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mrnm___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+ /* "csamtools.pyx":3203
+ * # read binary output
+ * out_stdout = inf.read()
+ * os.remove( stdout_f ) # <<<<<<<<<<<<<<
+ * else:
+ * out_stdout = []
+ */
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_f);
+ __Pyx_GIVEREF(__pyx_v_stdout_f);
+ __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L26;
}
-}
-
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
-}
+ /*else*/ {
-static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mpos___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+ /* "csamtools.pyx":3205
+ * os.remove( stdout_f )
+ * else:
+ * out_stdout = [] # <<<<<<<<<<<<<<
+ *
+ * # get error messages
+ */
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_out_stdout = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
}
-}
+ __pyx_L26:;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
-}
+ /* "csamtools.pyx":3208
+ *
+ * # get error messages
+ * pysam_unset_stderr() # <<<<<<<<<<<<<<
+ * try:
+ * with open( stderr_f, "r") as inf:
+ */
+ pysam_unset_stderr();
-static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5isize___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3209
+ * # get error messages
+ * pysam_unset_stderr()
+ * try: # <<<<<<<<<<<<<<
+ * with open( stderr_f, "r") as inf:
+ * out_stderr = inf.readlines()
+ */
+ {
+ __Pyx_ExceptionSave(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11);
+ __Pyx_XGOTREF(__pyx_t_9);
+ __Pyx_XGOTREF(__pyx_t_10);
+ __Pyx_XGOTREF(__pyx_t_11);
+ /*try:*/ {
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
-}
+ /* "csamtools.pyx":3210
+ * pysam_unset_stderr()
+ * try:
+ * with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError:
+ */
+ /*with:*/ {
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stderr_f);
+ __Pyx_GIVEREF(__pyx_v_stderr_f);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L83_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L83_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
+ __Pyx_XGOTREF(__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_17);
+ __Pyx_XGOTREF(__pyx_t_18);
+ /*try:*/ {
+ __Pyx_INCREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_v_inf);
+ __pyx_v_inf = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+
+ /* "csamtools.pyx":3211
+ * try:
+ * with open( stderr_f, "r") as inf:
+ * out_stderr = inf.readlines() # <<<<<<<<<<<<<<
+ * except UnicodeDecodeError:
+ * with open( stderr_f, "rb") as inf:
+ */
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L89_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L89_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_out_stderr = __pyx_t_3;
+ __pyx_t_3 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
+ __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
+ goto __pyx_L96_try_end;
+ __pyx_L89_error:;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+
+ /* "csamtools.pyx":3210
+ * pysam_unset_stderr()
+ * try:
+ * with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError:
+ */
+ /*except:*/ {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_INCREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ __Pyx_GOTREF(__pyx_t_19);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ __pyx_t_1 = (!__pyx_t_5);
+ if (__pyx_t_1) {
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __Pyx_ErrRestore(__pyx_t_3, __pyx_t_4, __pyx_t_2);
+ __pyx_t_3 = 0; __pyx_t_4 = 0; __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ goto __pyx_L100;
+ }
+ __pyx_L100:;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L90_exception_handled;
+ }
+ __pyx_L91_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
+ goto __pyx_L75_error;
+ __pyx_L90_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
+ __pyx_L96_try_end:;
+ }
+ }
+ /*finally:*/ {
+ if (__pyx_t_15) {
+ __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_183, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ __Pyx_GOTREF(__pyx_t_18);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
+ __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ }
+ }
+ goto __pyx_L101;
+ __pyx_L83_error:;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L75_error;
+ __pyx_L101:;
+ }
+ }
+ /*else:*/ {
-static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_paired___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3218
+ * os.remove( stderr_f )
+ * else:
+ * out_stderr = [] # <<<<<<<<<<<<<<
+ *
+ * return retval, out_stderr, out_stdout
+ */
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3218; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_v_out_stderr);
+ __pyx_v_out_stderr = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L82_try_end;
+ __pyx_L75_error:;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":3212
+ * with open( stderr_f, "r") as inf:
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError: # <<<<<<<<<<<<<<
+ * with open( stderr_f, "rb") as inf:
+ * # read binary output
+ */
+ __pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
+ if (__pyx_t_8) {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_3);
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
-}
+ /* "csamtools.pyx":3213
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError:
+ * with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
+ * # read binary output
+ * out_stderr = inf.read()
+ */
+ /*with:*/ {
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
+ __Pyx_GIVEREF(__pyx_v_stderr_f);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
+ __pyx_t_21 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_18);
+ __Pyx_XGOTREF(__pyx_t_17);
+ __Pyx_XGOTREF(__pyx_t_16);
+ /*try:*/ {
+ __Pyx_INCREF(__pyx_t_20);
+ __Pyx_XDECREF(__pyx_v_inf);
+ __pyx_v_inf = __pyx_t_20;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+
+ /* "csamtools.pyx":3215
+ * with open( stderr_f, "rb") as inf:
+ * # read binary output
+ * out_stderr = inf.read() # <<<<<<<<<<<<<<
+ * os.remove( stderr_f )
+ * else:
+ */
+ __pyx_t_20 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3215; __pyx_clineno = __LINE__; goto __pyx_L110_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3215; __pyx_clineno = __LINE__; goto __pyx_L110_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_v_out_stderr);
+ __pyx_v_out_stderr = __pyx_t_21;
+ __pyx_t_21 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
+ __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ goto __pyx_L117_try_end;
+ __pyx_L110_error:;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+
+ /* "csamtools.pyx":3213
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError:
+ * with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
+ * # read binary output
+ * out_stderr = inf.read()
+ */
+ /*except:*/ {
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_21, &__pyx_t_20, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_INCREF(__pyx_t_21);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_21);
+ __Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_INCREF(__pyx_t_20);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_20);
+ __Pyx_GIVEREF(__pyx_t_20);
+ __Pyx_INCREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
+ __Pyx_GOTREF(__pyx_t_19);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
+ __pyx_t_5 = (!__pyx_t_1);
+ if (__pyx_t_5) {
+ __Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_GIVEREF(__pyx_t_20);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_ErrRestore(__pyx_t_21, __pyx_t_20, __pyx_t_6);
+ __pyx_t_21 = 0; __pyx_t_20 = 0; __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
+ goto __pyx_L121;
+ }
+ __pyx_L121:;
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L111_exception_handled;
+ }
+ __pyx_L112_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
+ goto __pyx_L77_except_error;
+ __pyx_L111_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
+ __pyx_L117_try_end:;
+ }
+ }
+ /*finally:*/ {
+ if (__pyx_t_15) {
+ __pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_184, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_16);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
+ __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ }
+ }
+ goto __pyx_L122;
+ __pyx_L104_error:;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L77_except_error;
+ __pyx_L122:;
+ }
-static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3216
+ * # read binary output
+ * out_stderr = inf.read()
+ * os.remove( stderr_f ) # <<<<<<<<<<<<<<
+ * else:
+ * out_stderr = []
+ */
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_20 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__remove); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
+ __Pyx_GIVEREF(__pyx_v_stderr_f);
+ __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L76_exception_handled;
+ }
+ __pyx_L77_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
+ goto __pyx_L1_error;
+ __pyx_L76_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
+ __pyx_L82_try_end:;
+ }
+
+ /* "csamtools.pyx":3220
+ * out_stderr = []
+ *
+ * return retval, out_stderr, out_stdout # <<<<<<<<<<<<<<
+ *
+ * cdef class SNPCall:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_v_out_stderr);
+ PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_out_stderr);
+ __Pyx_GIVEREF(__pyx_v_out_stderr);
+ __Pyx_INCREF(__pyx_v_out_stdout);
+ PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_out_stdout);
+ __Pyx_GIVEREF(__pyx_v_out_stdout);
+ __pyx_t_3 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_4);
+ __pyx_t_4 = 0;
+ goto __pyx_L0;
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_20);
+ __Pyx_XDECREF(__pyx_t_21);
+ __Pyx_XDECREF(__pyx_t_22);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_stderr_h);
+ __Pyx_XDECREF(__pyx_v_stderr_f);
+ __Pyx_XDECREF(__pyx_v_stdout_h);
+ __Pyx_XDECREF(__pyx_v_stdout_f);
+ __Pyx_XDECREF(__pyx_v_stdout_save);
+ __Pyx_XDECREF(__pyx_v_inf);
+ __Pyx_XDECREF(__pyx_v_out_stdout);
+ __Pyx_XDECREF(__pyx_v_out_stderr);
+ __Pyx_XDECREF(__pyx_v_a);
+ __Pyx_XDECREF(__pyx_v_method);
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_catch_stdout);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_3tid___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
-}
+/* "csamtools.pyx":3235
+ * property tid:
+ * '''the chromosome ID as is defined in the header'''
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self._tid
+ *
+ */
-static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3235);
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
-}
+ /* "csamtools.pyx":3236
+ * '''the chromosome ID as is defined in the header'''
+ * def __get__(self):
+ * return self._tid # <<<<<<<<<<<<<<
+ *
+ * property pos:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_3pos___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+/* "csamtools.pyx":3240
+ * property pos:
+ * '''nucleotide position of SNP.'''
+ * def __get__(self): return self._pos # <<<<<<<<<<<<<<
+ *
+ * property reference_base:
+ */
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
-}
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3240);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read1___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read2___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+/* "csamtools.pyx":3244
+ * property reference_base:
+ * '''reference base at pos. ``N`` if no reference sequence supplied.'''
+ * def __get__(self): return from_string_and_size( &self._reference_base, 1 ) # <<<<<<<<<<<<<<
+ *
+ * property genotype:
+ */
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
-}
+static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3244);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&__pyx_v_self->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.reference_base.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_8genotype___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+/* "csamtools.pyx":3248
+ * property genotype:
+ * '''the genotype called.'''
+ * def __get__(self): return from_string_and_size( &self._genotype, 1 ) # <<<<<<<<<<<<<<
+ *
+ * property consensus_quality:
+ */
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
-}
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3248);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&__pyx_v_self->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.genotype.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
- {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_fancy_str)},
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = {
- {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_114), 0},
- {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_115), 0},
- {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_116), 0},
- {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_117), 0},
- {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_118), 0},
- {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_119), 0},
- {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_120), 0},
- {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_121), 0},
- {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_122), 0},
- {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_123), 0},
- {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_124), 0},
- {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_125), 0},
- {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_126), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_127), 0},
- {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_128), 0},
- {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_129), 0},
- {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_130), 0},
- {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_131), 0},
- {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_132), 0},
- {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_133), 0},
- {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_134), 0},
- {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_135), 0},
- {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_136), 0},
- {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_137), 0},
- {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_138), 0},
- {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_139), 0},
- {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_140), 0},
- {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_141), 0},
- {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_142), 0},
- {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_143), 0},
- {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_144), 0},
- {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_145), 0},
- {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_146), 0},
- {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_147), 0},
- {0, 0, 0, 0, 0}
-};
+/* "csamtools.pyx":3252
+ * property consensus_quality:
+ * '''the genotype quality (Phred-scaled).'''
+ * def __get__(self): return self._consensus_quality # <<<<<<<<<<<<<<
+ *
+ * property snp_quality:
+ */
-static PyNumberMethods __pyx_tp_as_number_AlignedRead = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_AlignedRead = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_AlignedRead = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-PyTypeObject __pyx_type_9csamtools_AlignedRead = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.AlignedRead"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_AlignedRead), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_AlignedRead, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_AlignedRead, /*tp_as_number*/
- &__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pf_9csamtools_11AlignedRead___hash__, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pf_9csamtools_11AlignedRead___str__, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for \n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
+static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3252);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_Samfile *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_Samfile *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
- if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.consensus_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_7Samfile___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- (*Py_TYPE(o)->tp_free)(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
-}
+/* "csamtools.pyx":3256
+ * property snp_quality:
+ * '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
+ * def __get__(self): return self._snp_quality # <<<<<<<<<<<<<<
+ *
+ * property mapping_quality:
+ */
-static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
-}
+static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3256);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.snp_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
+/* "csamtools.pyx":3260
+ * property mapping_quality:
+ * '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
+ * def __get__(self): return self._rms_mapping_quality # <<<<<<<<<<<<<<
+ *
+ * property coverage:
+ */
+
+static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3260);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.mapping_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall_8coverage___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__parseRegion)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___next__)},
- {0, 0, 0, 0}
-};
+/* "csamtools.pyx":3264
+ * property coverage:
+ * '''coverage or read depth - the number of reads involved in the call.'''
+ * def __get__(self): return self._coverage # <<<<<<<<<<<<<<
+ *
+ * def __str__(self):
+ */
-static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_148), 0},
- {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_149), 0},
- {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_150), 0},
- {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_151), 0},
- {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_152), 0},
- {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_153), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Samfile = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_Samfile = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_Samfile = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-PyTypeObject __pyx_type_9csamtools_Samfile = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_Samfile, /*tp_as_number*/
- &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*\n \n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n \n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary \n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output. \n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``. \n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open \n a :term:`BAM` formatted file for reading, type::\n\n f = pysam.Samfile('ex1.bam','rb')\n\n If mode is not specified, we will try to auto-detect in the order 'r', 'rb', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.bam' )\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile* \n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level \n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line \n being a list of tag-value pairs.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_7Samfile___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_7Samfile___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_Samfile, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3264);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
-static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- return o;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools.SNPCall.coverage.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
- (*Py_TYPE(o)->tp_free)(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_7SNPCall___str__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
-}
+/* "csamtools.pyx":3266
+ * def __get__(self): return self._coverage
+ *
+ * def __str__(self): # <<<<<<<<<<<<<<
+ *
+ * return "\t".join( map(str, (
+ */
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
-}
+static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 3266);
-static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11PileupProxy_1n___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
+ /* "csamtools.pyx":3268
+ * def __str__(self):
+ *
+ * return "\t".join( map(str, ( # <<<<<<<<<<<<<<
+ * self.tid,
+ * self.pos,
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
-}
+ /* "csamtools.pyx":3269
+ *
+ * return "\t".join( map(str, (
+ * self.tid, # <<<<<<<<<<<<<<
+ * self.pos,
+ * self.reference_base,
+ */
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
-}
+ /* "csamtools.pyx":3270
+ * return "\t".join( map(str, (
+ * self.tid,
+ * self.pos, # <<<<<<<<<<<<<<
+ * self.reference_base,
+ * self.genotype,
+ */
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
-static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
- {0, 0, 0, 0}
-};
+ /* "csamtools.pyx":3271
+ * self.tid,
+ * self.pos,
+ * self.reference_base, # <<<<<<<<<<<<<<
+ * self.genotype,
+ * self.consensus_quality,
+ */
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
-static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
- {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_155), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
- {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_156), 0},
- {0, 0, 0, 0, 0}
-};
+ /* "csamtools.pyx":3272
+ * self.pos,
+ * self.reference_base,
+ * self.genotype, # <<<<<<<<<<<<<<
+ * self.consensus_quality,
+ * self.snp_quality,
+ */
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
-static PyNumberMethods __pyx_tp_as_number_PileupProxy = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
+ /* "csamtools.pyx":3273
+ * self.reference_base,
+ * self.genotype,
+ * self.consensus_quality, # <<<<<<<<<<<<<<
+ * self.snp_quality,
+ * self.mapping_quality,
+ */
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
-static PyMappingMethods __pyx_tp_as_mapping_PileupProxy = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
+ /* "csamtools.pyx":3274
+ * self.genotype,
+ * self.consensus_quality,
+ * self.snp_quality, # <<<<<<<<<<<<<<
+ * self.mapping_quality,
+ * self.coverage ) ) )
+ */
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
-static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
+ /* "csamtools.pyx":3275
+ * self.consensus_quality,
+ * self.snp_quality,
+ * self.mapping_quality, # <<<<<<<<<<<<<<
+ * self.coverage ) ) )
+ *
+ */
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
-PyTypeObject __pyx_type_9csamtools_PileupProxy = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_PileupProxy, /*tp_as_number*/
- &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pf_9csamtools_11PileupProxy___str__, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column \n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
+ /* "csamtools.pyx":3276
+ * self.snp_quality,
+ * self.mapping_quality,
+ * self.coverage ) ) ) # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyTuple_New(8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_10, 4, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_10, 5, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_10, 6, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_10, 7, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_2 = 0;
+ __pyx_t_3 = 0;
+ __pyx_t_4 = 0;
+ __pyx_t_5 = 0;
+ __pyx_t_6 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
+ PyTuple_SET_ITEM(__pyx_t_9, 1, ((PyObject *)__pyx_t_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_r = __pyx_t_10;
+ __pyx_t_10 = 0;
+ goto __pyx_L0;
-static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_PileupRead *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_PileupRead *)o);
- p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
- return o;
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_AddTraceback("csamtools.SNPCall.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
- Py_XDECREF(((PyObject *)p->_alignment));
- (*Py_TYPE(o)->tp_free)(o);
-}
+/* Python wrapper */
+static int __pyx_pw_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ int __pyx_v_reopen;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ {
+ PyObject* values[2] = {0,0};
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reopen);
+ if (value) { values[1] = value; kw_args--; }
+ }
+ }
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ if (values[1]) {
+ } else {
-static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
- if (p->_alignment) {
- e = (*v)(((PyObject*)p->_alignment), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->_alignment);
- p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+ /* "csamtools.pyx":3786
+ * """
+ *
+ * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ *
+ */
+ __pyx_v_reopen = ((int)1);
+ }
+ } else {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ }
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ if (values[1]) {
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else {
+ __pyx_v_reopen = ((int)1);
+ }
+ }
+ goto __pyx_L4_argument_unpacking_done;
+ __pyx_L5_argtuple_error:;
+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_L3_error:;
+ __Pyx_AddTraceback("csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_RefNannyFinishContext();
+ return -1;
+ __pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_9csamtools_12IndexedReads___init__(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
-}
+static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ char *__pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3786);
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
-}
+ /* "csamtools.pyx":3787
+ *
+ * def __init__(self, Samfile samfile, int reopen = True ):
+ * self.samfile = samfile # <<<<<<<<<<<<<<
+ *
+ * if samfile.isbam: mode = b"rb"
+ */
+ __Pyx_INCREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
-}
+ /* "csamtools.pyx":3789
+ * self.samfile = samfile
+ *
+ * if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
+ * else: mode = b"r"
+ *
+ */
+ if (__pyx_v_samfile->isbam) {
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
+ __pyx_v_mode = __pyx_n_b__rb;
+ goto __pyx_L3;
+ }
+ /*else*/ {
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
-}
+ /* "csamtools.pyx":3790
+ *
+ * if samfile.isbam: mode = b"rb"
+ * else: mode = b"r" # <<<<<<<<<<<<<<
+ *
+ * # reopen the file - note that this makes the iterator
+ */
+ __Pyx_INCREF(((PyObject *)__pyx_n_b__r));
+ __pyx_v_mode = __pyx_n_b__r;
+ }
+ __pyx_L3:;
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
-}
+ /* "csamtools.pyx":3794
+ * # reopen the file - note that this makes the iterator
+ * # slow and causes pileup to slow down significantly.
+ * if reopen: # <<<<<<<<<<<<<<
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ */
+ if (__pyx_v_reopen) {
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
-}
+ /* "csamtools.pyx":3795
+ * # slow and causes pileup to slow down significantly.
+ * if reopen:
+ * store = StderrStore() # <<<<<<<<<<<<<<
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_store = __pyx_t_2;
+ __pyx_t_2 = 0;
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
-}
+ /* "csamtools.pyx":3796
+ * if reopen:
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
+ * store.release()
+ * assert self.fp != NULL
+ */
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
-static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
- {0, 0, 0, 0}
-};
+ /* "csamtools.pyx":3797
+ * store = StderrStore()
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release() # <<<<<<<<<<<<<<
+ * assert self.fp != NULL
+ * self.owns_samfile = True
+ */
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
- {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_157), 0},
- {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_158), 0},
- {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_159), 0},
- {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_160), 0},
- {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
- {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
- {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
- {0, 0, 0, 0, 0}
-};
+ /* "csamtools.pyx":3798
+ * self.fp = samopen( samfile._filename, mode, NULL )
+ * store.release()
+ * assert self.fp != NULL # <<<<<<<<<<<<<<
+ * self.owns_samfile = True
+ * else:
+ */
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ PyErr_SetNone(PyExc_AssertionError);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #endif
-static PyNumberMethods __pyx_tp_as_number_PileupRead = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
+ /* "csamtools.pyx":3799
+ * store.release()
+ * assert self.fp != NULL
+ * self.owns_samfile = True # <<<<<<<<<<<<<<
+ * else:
+ * self.fp = samfile.samfile
+ */
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L4;
+ }
+ /*else*/ {
-static PySequenceMethods __pyx_tp_as_sequence_PileupRead = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
+ /* "csamtools.pyx":3801
+ * self.owns_samfile = True
+ * else:
+ * self.fp = samfile.samfile # <<<<<<<<<<<<<<
+ * self.owns_samfile = False
+ *
+ */
+ __pyx_v_self->fp = __pyx_v_samfile->samfile;
-static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
+ /* "csamtools.pyx":3802
+ * else:
+ * self.fp = samfile.samfile
+ * self.owns_samfile = False # <<<<<<<<<<<<<<
+ *
+ * assert samfile.isbam, "can only IndexReads on bam files"
+ */
+ __pyx_v_self->owns_samfile = 0;
+ }
+ __pyx_L4:;
-static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
+ /* "csamtools.pyx":3804
+ * self.owns_samfile = False
+ *
+ * assert samfile.isbam, "can only IndexReads on bam files" # <<<<<<<<<<<<<<
+ *
+ * def build( self ):
+ */
+ #ifndef CYTHON_WITHOUT_ASSERTIONS
+ if (unlikely(!__pyx_v_samfile->isbam)) {
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_185));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
#endif
-};
-PyTypeObject __pyx_type_9csamtools_PileupRead = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_PileupRead, /*tp_as_number*/
- &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pf_9csamtools_10PileupRead___str__, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_PileupRead, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile;
-
-static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_Fastafile *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_Fastafile *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
- if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_mode);
+ __Pyx_XDECREF(__pyx_v_store);
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_9Fastafile___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- (*Py_TYPE(o)->tp_free)(o);
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_12IndexedReads_2build[] = "IndexedReads.build(self)\nbuild index.";
+static PyObject *__pyx_pw_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("build (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_12IndexedReads_2build(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
}
-static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
-}
+/* "csamtools.pyx":3806
+ * assert samfile.isbam, "can only IndexReads on bam files"
+ *
+ * def build( self ): # <<<<<<<<<<<<<<
+ * '''build index.'''
+ *
+ */
-static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__open)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_close)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_fetch)},
- {0, 0, 0, 0}
-};
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self) {
+ int __pyx_v_ret;
+ bam1_t *__pyx_v_b;
+ uint64_t __pyx_v_pos;
+ PyObject *__pyx_v_qname = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("build", 0);
+ __Pyx_TraceCall("build", __pyx_f[0], 3806);
-static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_148), 0},
- {0, 0, 0, 0, 0}
-};
+ /* "csamtools.pyx":3809
+ * '''build index.'''
+ *
+ * self.index = collections.defaultdict( list ) # <<<<<<<<<<<<<<
+ *
+ * # this method will start indexing from the current file position
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__collections); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)((PyObject*)(&PyList_Type))));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyList_Type))));
+ __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyList_Type))));
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_v_self->index);
+ __Pyx_DECREF(__pyx_v_self->index);
+ __pyx_v_self->index = __pyx_t_3;
+ __pyx_t_3 = 0;
-static PyNumberMethods __pyx_tp_as_number_Fastafile = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
+ /* "csamtools.pyx":3813
+ * # this method will start indexing from the current file position
+ * # if you decide
+ * cdef int ret = 1 # <<<<<<<<<<<<<<
+ * cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) )
+ *
+ */
+ __pyx_v_ret = 1;
-static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile___len__, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
+ /* "csamtools.pyx":3814
+ * # if you decide
+ * cdef int ret = 1
+ * cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
+ *
+ * cdef uint64_t pos
+ */
+ __pyx_v_b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
-static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile___len__, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
+ /* "csamtools.pyx":3818
+ * cdef uint64_t pos
+ *
+ * while ret > 0: # <<<<<<<<<<<<<<
+ * pos = bam_tell( self.fp.x.bam )
+ * ret = samread( self.fp, b)
+ */
+ while (1) {
+ __pyx_t_4 = (__pyx_v_ret > 0);
+ if (!__pyx_t_4) break;
-static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
+ /* "csamtools.pyx":3819
+ *
+ * while ret > 0:
+ * pos = bam_tell( self.fp.x.bam ) # <<<<<<<<<<<<<<
+ * ret = samread( self.fp, b)
+ * if ret > 0:
+ */
+ __pyx_v_pos = bam_tell(__pyx_v_self->fp->x.bam);
-PyTypeObject __pyx_type_9csamtools_Fastafile = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_Fastafile, /*tp_as_number*/
- &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(filename)*\n \n A *FASTA* file. The file is automatically opened.\n\n The file expects an indexed fasta file.\n\n TODO: \n add automatic indexing.\n add function to get sequence names.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
+ /* "csamtools.pyx":3820
+ * while ret > 0:
+ * pos = bam_tell( self.fp.x.bam )
+ * ret = samread( self.fp, b) # <<<<<<<<<<<<<<
+ * if ret > 0:
+ * qname = _charptr_to_str(bam1_qname( b ))
+ */
+ __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_b);
-static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
+ /* "csamtools.pyx":3821
+ * pos = bam_tell( self.fp.x.bam )
+ * ret = samread( self.fp, b)
+ * if ret > 0: # <<<<<<<<<<<<<<
+ * qname = _charptr_to_str(bam1_qname( b ))
+ * self.index[qname].append( pos )
+ */
+ __pyx_t_4 = (__pyx_v_ret > 0);
+ if (__pyx_t_4) {
+
+ /* "csamtools.pyx":3822
+ * ret = samread( self.fp, b)
+ * if ret > 0:
+ * qname = _charptr_to_str(bam1_qname( b )) # <<<<<<<<<<<<<<
+ * self.index[qname].append( pos )
+ *
+ */
+ __pyx_t_3 = __pyx_f_9csamtools__charptr_to_str(bam1_qname(__pyx_v_b)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_v_qname);
+ __pyx_v_qname = __pyx_t_3;
+ __pyx_t_3 = 0;
+
+ /* "csamtools.pyx":3823
+ * if ret > 0:
+ * qname = _charptr_to_str(bam1_qname( b ))
+ * self.index[qname].append( pos ) # <<<<<<<<<<<<<<
+ *
+ * bam_destroy1( b )
+ */
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint64_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_Append(__pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
+ }
+
+ /* "csamtools.pyx":3825
+ * self.index[qname].append( pos )
+ *
+ * bam_destroy1( b ) # <<<<<<<<<<<<<<
+ *
+ * def find( self, qname ):
+ */
+ bam_destroy1(__pyx_v_b);
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.IndexedReads.build", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_qname);
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static char __pyx_doc_9csamtools_12IndexedReads_4find[] = "IndexedReads.find(self, qname)";
+static PyObject *__pyx_pw_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("find (wrapper)", 0);
+ __pyx_r = __pyx_pf_9csamtools_12IndexedReads_4find(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "csamtools.pyx":3827
+ * bam_destroy1( b )
+ *
+ * def find( self, qname ): # <<<<<<<<<<<<<<
+ * if qname in self.index:
+ * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
+ */
+
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("find", 0);
+ __Pyx_TraceCall("find", __pyx_f[0], 3827);
+
+ /* "csamtools.pyx":3828
+ *
+ * def find( self, qname ):
+ * if qname in self.index: # <<<<<<<<<<<<<<
+ * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
+ * else:
+ */
+ __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->index, __pyx_v_qname))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+
+ /* "csamtools.pyx":3829
+ * def find( self, qname ):
+ * if qname in self.index:
+ * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False ) # <<<<<<<<<<<<<<
+ * else:
+ * raise KeyError( "read %s not found" % qname )
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_r = __pyx_t_4;
+ __pyx_t_4 = 0;
+ goto __pyx_L0;
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":3831
+ * return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
+ * else:
+ * raise KeyError( "read %s not found" % qname ) # <<<<<<<<<<<<<<
+ *
+ * def __dealloc__(self):
+ */
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_186), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_4, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L3:;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.IndexedReads.find", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "csamtools.pyx":3833
+ * raise KeyError( "read %s not found" % qname )
+ *
+ * def __dealloc__(self): # <<<<<<<<<<<<<<
+ * if self.owns_samfile: samclose( self.fp )
+ *
+ */
+
+static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3833);
+
+ /* "csamtools.pyx":3834
+ *
+ * def __dealloc__(self):
+ * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
+ *
+ * __all__ = ["Samfile",
+ */
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+}
+static struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile;
+
+static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Fastafile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools_Fastafile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
+ if (__pyx_pw_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_9csamtools_9Fastafile_11__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
+static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_9Fastafile_8filename_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_2_isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6_open)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_8close)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_13fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_12fetch)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRow = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Fastafile = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRow = {
- 0, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
+ __pyx_pw_9csamtools_9Fastafile_5__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = {
- 0, /*mp_length*/
+static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
+ __pyx_pw_9csamtools_9Fastafile_5__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
+static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorRow = {
+static PyTypeObject __pyx_type_9csamtools_Fastafile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRow, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRow, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Fastafile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n \n The method :meth:`Samfile.fetch` returns an IteratorRow.\n "), /*tp_doc*/
+ &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename)*\n\n A *FASTA* file. The file is automatically opened.\n\n The file expects an indexed fasta file.\n\n TODO:\n add automatic indexing.\n add function to get sequence names.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
+ __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRow, /*tp_new*/
+ __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_AlignedRead(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
+static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_17IteratorRowRegion___dealloc__(o);
+ __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->samfile));
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+ (*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(o, v);
}
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
- PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion___next__)},
- {0, 0, 0, 0}
-};
+static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
-static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(o);
+}
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
+static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(o);
+}
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
+static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
-PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_17IteratorRowRegion___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_17IteratorRowRegion___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(o);
+}
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAll *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
- if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
+static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_14IteratorRowAll___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5query_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll___next__)},
- {0, 0, 0, 0}
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(o);
+}
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(o);
+}
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(o);
+}
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(o);
+}
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(o);
+}
-PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorRowAll___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_14IteratorRowAll___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
+static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->rowiter));
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(o, v);
}
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- if (p->rowiter) {
- e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->rowiter);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs___next__)},
- {0, 0, 0, 0}
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(o);
+}
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
+static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(o);
+}
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(o);
+}
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(o);
+}
-PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(o);
+}
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
- p->positions = Py_None; Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
+static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- Py_XDECREF(p->positions);
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
}
- if (p->positions) {
- e = (*v)(p->positions, a); if (e) return e;
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
}
- tmp = ((PyObject*)p->positions);
- p->positions = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection___next__)},
- {0, 0, 0, 0}
-};
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(o);
+}
-static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
+static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
+ {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6compare)},
+ {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_10overlap)},
+ {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_12opt)},
+ {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_14fancy_str)},
+ {0, 0, 0, 0}
+};
+
+static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = {
+ {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0},
+ {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0},
+ {(char *)"cigarstring", __pyx_getprop_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0},
+ {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0},
+ {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0},
+ {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0},
+ {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0},
+ {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0},
+ {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0},
+ {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
+ {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0},
+ {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0},
+ {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0},
+ {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0},
+ {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0},
+ {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
+ {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
+ {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0},
+ {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0},
+ {(char *)"rnext", __pyx_getprop_9csamtools_11AlignedRead_rnext, __pyx_setprop_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0},
+ {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0},
+ {(char *)"pnext", __pyx_getprop_9csamtools_11AlignedRead_pnext, __pyx_setprop_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0},
+ {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0},
+ {(char *)"tlen", __pyx_getprop_9csamtools_11AlignedRead_tlen, __pyx_setprop_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0},
+ {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0},
+ {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0},
+ {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0},
+ {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0},
+ {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0},
+ {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0},
+ {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0},
+ {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0},
+ {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0},
+ {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0},
+ {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0},
+ {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
+ {(char *)"aligned_pairs", __pyx_getprop_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_AlignedRead = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
0, /*nb_inplace_remainder*/
0, /*nb_inplace_power*/
0, /*nb_inplace_lshift*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
+static PySequenceMethods __pyx_tp_as_sequence_AlignedRead = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
+static PyMappingMethods __pyx_tp_as_mapping_AlignedRead = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
+static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
+static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.AlignedRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_AlignedRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_AlignedRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
- 0, /*tp_hash*/
+ &__pyx_tp_as_number_AlignedRead, /*tp_as_number*/
+ &__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
+ __pyx_pw_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pw_9csamtools_11AlignedRead_5__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
+ &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for\n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n\n In Python 3, the fields containing sequence and quality\n (seq, query, qual and qqual) data are of type bytes. Other\n string data, such as the qname field and strings in the\n tags tuple, is represented as unicode strings. On assignment,\n both bytes and unicode objects are allowed, but unicode strings\n must contain only ASCII characters.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_20IteratorRowSelection___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorRowSelection___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pw_9csamtools_11AlignedRead_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
+ __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumn *p;
+static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Samfile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
- p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
- p->stepper = Py_None; Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_Samfile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
+ if (__pyx_pw_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
+static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_14IteratorColumn___dealloc__(o);
+ __pyx_pw_9csamtools_7Samfile_31__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->iter));
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->fastafile));
- Py_XDECREF(p->stepper);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
- if (p->iter) {
- e = (*v)(((PyObject*)p->iter), a); if (e) return e;
- }
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- if (p->fastafile) {
- e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
- }
- if (p->stepper) {
- e = (*v)(p->stepper, a); if (e) return e;
- }
- return 0;
+static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_8filename_1__get__(o);
}
-static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->fastafile);
- p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->stepper);
- p->stepper = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_10references_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_hasReference)},
+static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_7lengths_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_6mapped_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_4text_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_6header_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4_hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12_parseRegion)},
+ {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14reset)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_20fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_22mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_24count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_26pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_28close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_32write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_34__enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_36__exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_38_buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_42__next__)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_161), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
+ {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
+ {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
+ {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
+ {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
+ {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
+ {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
+ {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
{0, 0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
+static PyNumberMethods __pyx_tp_as_number_Samfile = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
+static PySequenceMethods __pyx_tp_as_sequence_Samfile = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
+static PyMappingMethods __pyx_tp_as_mapping_Samfile = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
+static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
+static PyTypeObject __pyx_type_9csamtools_Samfile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Samfile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n \n For reasons of efficiency, the iterator points to the current \n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n \n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, \n but each object in ``result`` will contain the same information.\n \n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n \n \n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,\n add_sq_text = False, check_header = True, check_sq = True )*\n\n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n\n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary\n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output.\n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``.\n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open\n a :term:`BAM` formatted file for reading, type::\n\n f = pysam.Samfile('ex1.bam','rb')\n\n If mode is not specified, we will try to auto-detect in the order 'rb', 'r', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.sam' )\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile*\n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level\n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line\n being a list of tag-value pairs. The header is constructed first from all the defined fields,\n followed by user tags in alphabetical order.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n By default, 'SQ' and 'LN' tags will be added to the header text. This option can be\n changed by unsetting the flag *add_sq_text*. \n\n By default, if file a file is opened in mode 'r', it is checked for a valid header\n (*check_header* = True) and a definition of chromosome names (*check_sq* = True). \n \n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorColumn___iter__, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
+ __pyx_pw_9csamtools_7Samfile_41__iter__, /*tp_iter*/
+ __pyx_pw_9csamtools_7Samfile_43__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
+ __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
+ __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
- if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion___next__)},
+static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11PileupProxy_1n_1__get__(o);
+}
+
+static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
+ {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_PileupProxy = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
+static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupProxy = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
+static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/
+ &__pyx_tp_as_number_PileupProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pw_9csamtools_11PileupProxy_3__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorColumnRegion___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pw_9csamtools_11PileupProxy_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_PileupRead *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
+ p = ((struct __pyx_obj_9csamtools_PileupRead *)o);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs___next__)},
+static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ Py_XDECREF(((PyObject *)p->_alignment));
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ if (p->_alignment) {
+ e = (*v)(((PyObject*)p->_alignment), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->_alignment);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_5indel_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_10PileupRead_5level_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
+ {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
+ {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
+ {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
+ {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
+ {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
+ {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
+ {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_PileupRead = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_PileupRead = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_PileupRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/
+ &__pyx_tp_as_number_PileupRead, /*tp_as_number*/
+ &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pw_9csamtools_10PileupRead_3__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pf_9csamtools_21IteratorColumnAllRefs___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_PileupRead, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pw_9csamtools_10PileupRead_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0},
- {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_163), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_165), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_166), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_167), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_168), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_SNPCall = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRow = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRow = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCall = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_SNPCall = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRow, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCall, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRow, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
+ &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n\n The method :meth:`Samfile.fetch` returns an IteratorRow.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRow, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_vtable_9csamtools_SNPCallerBase;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_9csamtools_SNPCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_SNPCallerBase *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_SNPCallerBase *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_SNPCallerBase;
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_13SNPCallerBase___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_SNPCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_13SNPCallerBase___dealloc__(o);
+ __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->iter));
- (*Py_TYPE(o)->tp_free)(o);
+ Py_XDECREF(((PyObject *)p->samfile));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_SNPCallerBase(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
- if (p->iter) {
- e = (*v)(((PyObject*)p->iter), a); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_SNPCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
PyObject* tmp;
- tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_SNPCallerBase[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_SNPCallerBase = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCallerBase = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCallerBase = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCallerBase = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_SNPCallerBase = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCallerBase"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCallerBase), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCallerBase, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCallerBase, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCallerBase, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCallerBase, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("Base class for SNP callers.\n\n *min_baseQ*\n minimum base quality (possibly capped by BAQ)\n *capQ_threshold*\n coefficient for adjusting mapQ of poor mappings\n *theta*\n theta in maq consensus calling model\n *n_haplotypes*\n number of haplotypes in the sample\n *het_rate*\n prior of a difference between two haplotypes\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between\n samfile and the iterator.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCallerBase, /*tp_methods*/
+ __pyx_pw_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/
+ __pyx_pw_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCallerBase, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls __pyx_vtable_9csamtools_IteratorSNPCalls;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-static PyObject *__pyx_tp_new_9csamtools_IteratorSNPCalls(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorSNPCalls *p;
- PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAll *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_IteratorSNPCalls;
- if (__pyx_pf_9csamtools_16IteratorSNPCalls___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
+ if (__pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorSNPCalls[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_16IteratorSNPCalls___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_16IteratorSNPCalls___next__)},
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorSNPCalls = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorSNPCalls = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorSNPCalls = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorSNPCalls = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorSNPCalls = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorSNPCalls"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorSNPCalls), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorSNPCalls, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorSNPCalls, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorSNPCalls, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorSNPCalls, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(IteratorColumn iterator)*\n\n call SNPs within a region.\n\n *iterator* is a pileup iterator. SNPs will be called\n on all positions returned by this iterator.\n\n This caller is fast if SNPs are called over large continuous\n regions. It is slow, if instantiated frequently and in random\n order as the sequence will have to be reloaded.\n\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_16IteratorSNPCalls___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_16IteratorSNPCalls___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorSNPCalls, /*tp_methods*/
+ __pyx_pw_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/
+ __pyx_pw_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorSNPCalls, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_SNPCaller __pyx_vtable_9csamtools_SNPCaller;
-static PyObject *__pyx_tp_new_9csamtools_SNPCaller(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_SNPCaller *p;
- PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_SNPCaller *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_SNPCaller;
- if (__pyx_pf_9csamtools_9SNPCaller___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_SNPCaller[] = {
- {__Pyx_NAMESTR("call"), (PyCFunction)__pyx_pf_9csamtools_9SNPCaller_call, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9SNPCaller_call)},
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->rowiter));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->rowiter) {
+ e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->rowiter);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_2nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_SNPCaller = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCaller = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCaller = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCaller = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_SNPCaller = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCaller"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCaller), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCaller, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCaller, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCaller, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCaller, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(IteratorColumn iterator_column )*\n\n The samtools SNP caller.\n\n This object will call SNPs in *samfile* against the reference\n sequence in *fasta*.\n\n This caller is fast for calling few SNPs in selected regions.\n\n It is slow, if called over large genomic regions.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCaller, /*tp_methods*/
+ __pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/
+ __pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCaller, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_9csamtools_IndelCall(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- if (__pyx_pf_9csamtools_9IndelCall___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
+ p->positions = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IndelCall(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_9IndelCall___dealloc__(o);
+ __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_3tid___get__(o);
+ Py_XDECREF(p->positions);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_3pos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_genotype(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_8genotype___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_17consensus_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_11snp_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_15mapping_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_coverage(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_8coverage___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_first_allele(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_12first_allele___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_second_allele(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_13second_allele___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_first(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_11reads_first___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_second(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_12reads_second___get__(o);
+static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->positions) {
+ e = (*v)(p->positions, a); if (e) return e;
+ }
+ return 0;
}
-static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_diff(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9IndelCall_10reads_diff___get__(o);
+static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->positions);
+ p->positions = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IndelCall[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_4__next__)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_IndelCall[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_9IndelCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_9IndelCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_9IndelCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_9IndelCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_165), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_9IndelCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_166), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_9IndelCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_167), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_9IndelCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_168), 0},
- {(char *)"first_allele", __pyx_getprop_9csamtools_9IndelCall_first_allele, 0, __Pyx_DOCSTR(__pyx_k_169), 0},
- {(char *)"second_allele", __pyx_getprop_9csamtools_9IndelCall_second_allele, 0, __Pyx_DOCSTR(__pyx_k_170), 0},
- {(char *)"reads_first", __pyx_getprop_9csamtools_9IndelCall_reads_first, 0, __Pyx_DOCSTR(__pyx_k_171), 0},
- {(char *)"reads_second", __pyx_getprop_9csamtools_9IndelCall_reads_second, 0, __Pyx_DOCSTR(__pyx_k_171), 0},
- {(char *)"reads_diff", __pyx_getprop_9csamtools_9IndelCall_reads_diff, 0, __Pyx_DOCSTR(__pyx_k_171), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IndelCall = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndelCall = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndelCall = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndelCall = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndelCall = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndelCall"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndelCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndelCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IndelCall, /*tp_as_number*/
- &__pyx_tp_as_sequence_IndelCall, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IndelCall, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_9IndelCall___str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IndelCall, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("the results of an indel call."), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IndelCall, /*tp_methods*/
+ __pyx_pw_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/
+ __pyx_pw_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_IndelCall, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IndelCall, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
-static PyObject *__pyx_tp_new_9csamtools_IndelCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IndelCallerBase *p;
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IndelCallerBase *)o);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_15IndelCallerBase___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p->stepper = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pw_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IndelCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_15IndelCallerBase___dealloc__(o);
+ __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
Py_XDECREF(((PyObject *)p->iter));
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->fastafile));
+ Py_XDECREF(p->stepper);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools_IndelCallerBase(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o;
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
if (p->iter) {
e = (*v)(((PyObject*)p->iter), a); if (e) return e;
}
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->fastafile) {
+ e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
+ }
+ if (p->stepper) {
+ e = (*v)(p->stepper, a); if (e) return e;
+ }
return 0;
}
-static int __pyx_tp_clear_9csamtools_IndelCallerBase(PyObject *o) {
- struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o;
+static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
PyObject* tmp;
tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None);
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->fastafile);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->stepper);
+ p->stepper = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IndelCallerBase[] = {
- {__Pyx_NAMESTR("_call"), (PyCFunction)__pyx_pf_9csamtools_15IndelCallerBase__call, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_15IndelCallerBase__call)},
+static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
+ {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_4addReference)},
+ {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_6hasReference)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndelCallerBase = {
+static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
+ {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndelCallerBase = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndelCallerBase = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndelCallerBase = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndelCallerBase = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndelCallerBase"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndelCallerBase), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IndelCallerBase, /*tp_as_number*/
- &__pyx_tp_as_sequence_IndelCallerBase, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IndelCallerBase, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IndelCallerBase, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("Base class for SNP callers.\n\n *min_baseQ*\n minimum base quality (possibly capped by BAQ)\n *capQ_threshold*\n coefficient for adjusting mapQ of poor mappings\n *theta*\n theta in maq consensus calling model\n *n_haplotypes*\n number of haplotypes in the sample\n *het_rate*\n prior of a difference between two haplotypes\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n\n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns,\n but each object in ``result`` will contain the same information.\n\n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controls how the iterator advances.\n Possible options for the stepper are\n\n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n\n The default is to use \"all\" if no stepper is given.\n\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
+ __pyx_pw_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_IndelCallerBase, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IndelCallerBase, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_9csamtools_IndelCaller(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_9csamtools_IndelCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- if (__pyx_pf_9csamtools_11IndelCaller___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
+ if (__pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IndelCaller[] = {
- {__Pyx_NAMESTR("call"), (PyCFunction)__pyx_pf_9csamtools_11IndelCaller_call, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11IndelCaller_call)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_2__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndelCaller = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndelCaller = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndelCaller = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndelCaller = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndelCaller = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndelCaller"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndelCaller), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IndelCaller, /*tp_as_number*/
- &__pyx_tp_as_sequence_IndelCaller, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IndelCaller, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IndelCaller, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(IteratorColumn iterator_column )*\n\n The samtools SNP caller.\n\n This object will call SNPs in *samfile* against the reference\n sequence in *fasta*.\n\n This caller is fast for calling few SNPs in selected regions.\n\n It is slow, if called over large genomic regions.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IndelCaller, /*tp_methods*/
+ __pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IndelCaller, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_9csamtools_IteratorIndelCalls(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_9csamtools_IndelCallerBase(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- if (__pyx_pf_9csamtools_18IteratorIndelCalls___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
+ if (__pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorIndelCalls[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorIndelCalls___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorIndelCalls___next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorIndelCalls = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorIndelCalls = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorIndelCalls = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorIndelCalls = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorIndelCalls = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorIndelCalls"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorIndelCalls), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorIndelCalls, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorIndelCalls, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorIndelCalls, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorIndelCalls, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(IteratorColumn iterator)*\n\n call indels within a region.\n\n *iterator* is a pileup iterator. SNPs will be called\n on all positions returned by this iterator.\n\n This caller is fast if SNPs are called over large continuous\n regions. It is slow, if instantiated frequently and in random\n order as the sequence will have to be reloaded.\n\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_18IteratorIndelCalls___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_18IteratorIndelCalls___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorIndelCalls, /*tp_methods*/
+ 0, /*tp_iter*/
+ __pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorIndelCalls, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_12IndexedReads___dealloc__(o);
+ __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
- {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_build)},
- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_find)},
+ {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2build)},
+ {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_4find)},
{0, 0, 0, 0}
};
#endif
};
-PyTypeObject __pyx_type_9csamtools_IndexedReads = {
+static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/
sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
__pyx_tp_traverse_9csamtools_IndexedReads, /*tp_traverse*/
__pyx_tp_clear_9csamtools_IndexedReads, /*tp_clear*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/
+ __pyx_pw_9csamtools_12IndexedReads_1__init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/
0, /*tp_free*/
#endif
};
-static PyMethodDef __pyx_methods[] = {
- {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pf_9csamtools__samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools__samtools_dispatch)},
+static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_3tid_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_3pos_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
{0, 0, 0, 0}
};
-#if PY_MAJOR_VERSION >= 3
-static struct PyModuleDef __pyx_moduledef = {
- PyModuleDef_HEAD_INIT,
- __Pyx_NAMESTR("csamtools"),
- 0, /* m_doc */
- -1, /* m_size */
- __pyx_methods /* m_methods */,
- NULL, /* m_reload */
- NULL, /* m_traverse */
- NULL, /* m_clear */
- NULL /* m_free */
+static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
+ {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
+ {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
+ {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
+ {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
+ {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
+ {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
+ {0, 0, 0, 0, 0}
};
-#endif
-static __Pyx_StringTabEntry __pyx_string_tab[] = {
- {&__pyx_kp_s_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 1, 0},
- {&__pyx_kp_s_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 1, 0},
- {&__pyx_kp_s_100, __pyx_k_100, sizeof(__pyx_k_100), 0, 0, 1, 0},
- {&__pyx_kp_s_101, __pyx_k_101, sizeof(__pyx_k_101), 0, 0, 1, 0},
- {&__pyx_kp_s_102, __pyx_k_102, sizeof(__pyx_k_102), 0, 0, 1, 0},
- {&__pyx_n_s_103, __pyx_k_103, sizeof(__pyx_k_103), 0, 0, 1, 1},
- {&__pyx_kp_s_104, __pyx_k_104, sizeof(__pyx_k_104), 0, 0, 1, 0},
- {&__pyx_kp_s_105, __pyx_k_105, sizeof(__pyx_k_105), 0, 0, 1, 0},
- {&__pyx_kp_s_107, __pyx_k_107, sizeof(__pyx_k_107), 0, 0, 1, 0},
- {&__pyx_kp_s_108, __pyx_k_108, sizeof(__pyx_k_108), 0, 0, 1, 0},
- {&__pyx_kp_s_109, __pyx_k_109, sizeof(__pyx_k_109), 0, 0, 1, 0},
- {&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0},
- {&__pyx_kp_s_110, __pyx_k_110, sizeof(__pyx_k_110), 0, 0, 1, 0},
- {&__pyx_kp_s_111, __pyx_k_111, sizeof(__pyx_k_111), 0, 0, 1, 0},
- {&__pyx_kp_s_112, __pyx_k_112, sizeof(__pyx_k_112), 0, 0, 1, 0},
- {&__pyx_kp_s_113, __pyx_k_113, sizeof(__pyx_k_113), 0, 0, 1, 0},
- {&__pyx_kp_s_12, __pyx_k_12, sizeof(__pyx_k_12), 0, 0, 1, 0},
- {&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
- {&__pyx_kp_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 0},
- {&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0},
- {&__pyx_kp_s_174, __pyx_k_174, sizeof(__pyx_k_174), 0, 0, 1, 0},
- {&__pyx_kp_s_175, __pyx_k_175, sizeof(__pyx_k_175), 0, 0, 1, 0},
- {&__pyx_kp_s_176, __pyx_k_176, sizeof(__pyx_k_176), 0, 0, 1, 0},
- {&__pyx_kp_u_177, __pyx_k_177, sizeof(__pyx_k_177), 0, 1, 0, 0},
- {&__pyx_kp_u_178, __pyx_k_178, sizeof(__pyx_k_178), 0, 1, 0, 0},
- {&__pyx_kp_u_179, __pyx_k_179, sizeof(__pyx_k_179), 0, 1, 0, 0},
- {&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
- {&__pyx_kp_u_180, __pyx_k_180, sizeof(__pyx_k_180), 0, 1, 0, 0},
- {&__pyx_kp_u_181, __pyx_k_181, sizeof(__pyx_k_181), 0, 1, 0, 0},
- {&__pyx_kp_u_182, __pyx_k_182, sizeof(__pyx_k_182), 0, 1, 0, 0},
- {&__pyx_kp_u_183, __pyx_k_183, sizeof(__pyx_k_183), 0, 1, 0, 0},
- {&__pyx_kp_u_184, __pyx_k_184, sizeof(__pyx_k_184), 0, 1, 0, 0},
- {&__pyx_kp_u_185, __pyx_k_185, sizeof(__pyx_k_185), 0, 1, 0, 0},
- {&__pyx_kp_u_186, __pyx_k_186, sizeof(__pyx_k_186), 0, 1, 0, 0},
- {&__pyx_kp_u_187, __pyx_k_187, sizeof(__pyx_k_187), 0, 1, 0, 0},
- {&__pyx_kp_u_188, __pyx_k_188, sizeof(__pyx_k_188), 0, 1, 0, 0},
- {&__pyx_kp_u_189, __pyx_k_189, sizeof(__pyx_k_189), 0, 1, 0, 0},
- {&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
- {&__pyx_kp_u_190, __pyx_k_190, sizeof(__pyx_k_190), 0, 1, 0, 0},
- {&__pyx_kp_u_191, __pyx_k_191, sizeof(__pyx_k_191), 0, 1, 0, 0},
- {&__pyx_kp_u_192, __pyx_k_192, sizeof(__pyx_k_192), 0, 1, 0, 0},
- {&__pyx_kp_u_193, __pyx_k_193, sizeof(__pyx_k_193), 0, 1, 0, 0},
- {&__pyx_kp_u_194, __pyx_k_194, sizeof(__pyx_k_194), 0, 1, 0, 0},
- {&__pyx_kp_u_195, __pyx_k_195, sizeof(__pyx_k_195), 0, 1, 0, 0},
- {&__pyx_kp_u_196, __pyx_k_196, sizeof(__pyx_k_196), 0, 1, 0, 0},
- {&__pyx_kp_u_197, __pyx_k_197, sizeof(__pyx_k_197), 0, 1, 0, 0},
- {&__pyx_kp_u_198, __pyx_k_198, sizeof(__pyx_k_198), 0, 1, 0, 0},
- {&__pyx_kp_u_199, __pyx_k_199, sizeof(__pyx_k_199), 0, 1, 0, 0},
- {&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
- {&__pyx_kp_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 0},
- {&__pyx_n_s_200, __pyx_k_200, sizeof(__pyx_k_200), 0, 0, 1, 1},
- {&__pyx_kp_u_201, __pyx_k_201, sizeof(__pyx_k_201), 0, 1, 0, 0},
- {&__pyx_kp_u_202, __pyx_k_202, sizeof(__pyx_k_202), 0, 1, 0, 0},
- {&__pyx_kp_u_203, __pyx_k_203, sizeof(__pyx_k_203), 0, 1, 0, 0},
- {&__pyx_n_s_204, __pyx_k_204, sizeof(__pyx_k_204), 0, 0, 1, 1},
- {&__pyx_kp_u_205, __pyx_k_205, sizeof(__pyx_k_205), 0, 1, 0, 0},
- {&__pyx_n_s_206, __pyx_k_206, sizeof(__pyx_k_206), 0, 0, 1, 1},
- {&__pyx_kp_u_207, __pyx_k_207, sizeof(__pyx_k_207), 0, 1, 0, 0},
- {&__pyx_kp_u_208, __pyx_k_208, sizeof(__pyx_k_208), 0, 1, 0, 0},
- {&__pyx_kp_u_209, __pyx_k_209, sizeof(__pyx_k_209), 0, 1, 0, 0},
- {&__pyx_kp_s_21, __pyx_k_21, sizeof(__pyx_k_21), 0, 0, 1, 0},
- {&__pyx_kp_u_210, __pyx_k_210, sizeof(__pyx_k_210), 0, 1, 0, 0},
- {&__pyx_kp_u_211, __pyx_k_211, sizeof(__pyx_k_211), 0, 1, 0, 0},
- {&__pyx_kp_u_212, __pyx_k_212, sizeof(__pyx_k_212), 0, 1, 0, 0},
- {&__pyx_kp_u_213, __pyx_k_213, sizeof(__pyx_k_213), 0, 1, 0, 0},
- {&__pyx_kp_u_214, __pyx_k_214, sizeof(__pyx_k_214), 0, 1, 0, 0},
- {&__pyx_kp_u_215, __pyx_k_215, sizeof(__pyx_k_215), 0, 1, 0, 0},
- {&__pyx_kp_u_216, __pyx_k_216, sizeof(__pyx_k_216), 0, 1, 0, 0},
- {&__pyx_kp_u_217, __pyx_k_217, sizeof(__pyx_k_217), 0, 1, 0, 0},
- {&__pyx_kp_u_218, __pyx_k_218, sizeof(__pyx_k_218), 0, 1, 0, 0},
- {&__pyx_kp_u_219, __pyx_k_219, sizeof(__pyx_k_219), 0, 1, 0, 0},
- {&__pyx_kp_s_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 1, 0},
- {&__pyx_kp_u_220, __pyx_k_220, sizeof(__pyx_k_220), 0, 1, 0, 0},
- {&__pyx_kp_s_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 1, 0},
- {&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
- {&__pyx_kp_s_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 1, 0},
- {&__pyx_kp_s_26, __pyx_k_26, sizeof(__pyx_k_26), 0, 0, 1, 0},
- {&__pyx_kp_s_27, __pyx_k_27, sizeof(__pyx_k_27), 0, 0, 1, 0},
- {&__pyx_kp_s_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 1, 0},
- {&__pyx_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0},
- {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
- {&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
- {&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
- {&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0},
- {&__pyx_kp_s_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 1, 0},
- {&__pyx_kp_s_35, __pyx_k_35, sizeof(__pyx_k_35), 0, 0, 1, 0},
- {&__pyx_kp_s_36, __pyx_k_36, sizeof(__pyx_k_36), 0, 0, 1, 0},
- {&__pyx_kp_s_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 1, 0},
- {&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0},
- {&__pyx_kp_s_4, __pyx_k_4, sizeof(__pyx_k_4), 0, 0, 1, 0},
- {&__pyx_kp_s_40, __pyx_k_40, sizeof(__pyx_k_40), 0, 0, 1, 0},
- {&__pyx_kp_s_41, __pyx_k_41, sizeof(__pyx_k_41), 0, 0, 1, 0},
- {&__pyx_kp_s_42, __pyx_k_42, sizeof(__pyx_k_42), 0, 0, 1, 0},
- {&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0},
- {&__pyx_kp_s_44, __pyx_k_44, sizeof(__pyx_k_44), 0, 0, 1, 0},
- {&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0},
- {&__pyx_kp_s_46, __pyx_k_46, sizeof(__pyx_k_46), 0, 0, 1, 0},
- {&__pyx_kp_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 0},
- {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0},
- {&__pyx_kp_s_49, __pyx_k_49, sizeof(__pyx_k_49), 0, 0, 1, 0},
- {&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0},
+static PyNumberMethods __pyx_tp_as_number_SNPCall = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_SNPCall = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_9csamtools_SNPCall = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_SNPCall, /*tp_as_number*/
+ &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ __pyx_pw_9csamtools_7SNPCall_1__str__, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o);
+ p->__pyx_v_x = 0;
+ p->__pyx_v_y = 0;
+ p->__pyx_t_0 = 0;
+ p->__pyx_t_1 = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+ Py_XDECREF(p->__pyx_v_x);
+ Py_XDECREF(p->__pyx_v_y);
+ Py_XDECREF(p->__pyx_t_0);
+ Py_XDECREF(p->__pyx_t_1);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+ if (p->__pyx_v_x) {
+ e = (*v)(p->__pyx_v_x, a); if (e) return e;
+ }
+ if (p->__pyx_v_y) {
+ e = (*v)(p->__pyx_v_y, a); if (e) return e;
+ }
+ if (p->__pyx_t_0) {
+ e = (*v)(p->__pyx_t_0, a); if (e) return e;
+ }
+ if (p->__pyx_t_1) {
+ e = (*v)(p->__pyx_t_1, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->__pyx_v_x);
+ p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_v_y);
+ p->__pyx_v_y = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_0);
+ p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_1);
+ p->__pyx_t_1 = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct__genexpr[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__genexpr = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__genexpr = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct__genexpr = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_scope_struct__genexpr, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct__genexpr, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct__genexpr, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_scope_struct__genexpr, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o);
+ p->__pyx_v_x = 0;
+ p->__pyx_v_y = 0;
+ p->__pyx_t_0 = 0;
+ p->__pyx_t_1 = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ Py_XDECREF(p->__pyx_v_x);
+ Py_XDECREF(p->__pyx_v_y);
+ Py_XDECREF(p->__pyx_t_0);
+ Py_XDECREF(p->__pyx_t_1);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ if (p->__pyx_v_x) {
+ e = (*v)(p->__pyx_v_x, a); if (e) return e;
+ }
+ if (p->__pyx_v_y) {
+ e = (*v)(p->__pyx_v_y, a); if (e) return e;
+ }
+ if (p->__pyx_t_0) {
+ e = (*v)(p->__pyx_t_0, a); if (e) return e;
+ }
+ if (p->__pyx_t_1) {
+ e = (*v)(p->__pyx_t_1, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->__pyx_v_x);
+ p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_v_y);
+ p->__pyx_v_y = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_0);
+ p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_1);
+ p->__pyx_t_1 = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_1_genexpr = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_scope_struct_1_genexpr, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct_1_genexpr, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct_1_genexpr, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyMethodDef __pyx_methods[] = {
+ {0, 0, 0, 0}
+};
+
+#if PY_MAJOR_VERSION >= 3
+static struct PyModuleDef __pyx_moduledef = {
+ PyModuleDef_HEAD_INIT,
+ __Pyx_NAMESTR("csamtools"),
+ 0, /* m_doc */
+ -1, /* m_size */
+ __pyx_methods /* m_methods */,
+ NULL, /* m_reload */
+ NULL, /* m_traverse */
+ NULL, /* m_clear */
+ NULL /* m_free */
+};
+#endif
+
+static __Pyx_StringTabEntry __pyx_string_tab[] = {
+ {&__pyx_kp_u_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 1, 0, 0},
+ {&__pyx_kp_s_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 1, 0},
+ {&__pyx_kp_s_100, __pyx_k_100, sizeof(__pyx_k_100), 0, 0, 1, 0},
+ {&__pyx_kp_s_102, __pyx_k_102, sizeof(__pyx_k_102), 0, 0, 1, 0},
+ {&__pyx_kp_s_104, __pyx_k_104, sizeof(__pyx_k_104), 0, 0, 1, 0},
+ {&__pyx_kp_s_105, __pyx_k_105, sizeof(__pyx_k_105), 0, 0, 1, 0},
+ {&__pyx_kp_s_107, __pyx_k_107, sizeof(__pyx_k_107), 0, 0, 1, 0},
+ {&__pyx_kp_s_108, __pyx_k_108, sizeof(__pyx_k_108), 0, 0, 1, 0},
+ {&__pyx_kp_s_109, __pyx_k_109, sizeof(__pyx_k_109), 0, 0, 1, 0},
+ {&__pyx_kp_s_110, __pyx_k_110, sizeof(__pyx_k_110), 0, 0, 1, 0},
+ {&__pyx_kp_s_111, __pyx_k_111, sizeof(__pyx_k_111), 0, 0, 1, 0},
+ {&__pyx_kp_s_113, __pyx_k_113, sizeof(__pyx_k_113), 0, 0, 1, 0},
+ {&__pyx_kp_s_116, __pyx_k_116, sizeof(__pyx_k_116), 0, 0, 1, 0},
+ {&__pyx_kp_s_119, __pyx_k_119, sizeof(__pyx_k_119), 0, 0, 1, 0},
+ {&__pyx_kp_s_125, __pyx_k_125, sizeof(__pyx_k_125), 0, 0, 1, 0},
+ {&__pyx_kp_s_126, __pyx_k_126, sizeof(__pyx_k_126), 0, 0, 1, 0},
+ {&__pyx_kp_s_127, __pyx_k_127, sizeof(__pyx_k_127), 0, 0, 1, 0},
+ {&__pyx_kp_s_129, __pyx_k_129, sizeof(__pyx_k_129), 0, 0, 1, 0},
+ {&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
+ {&__pyx_kp_s_135, __pyx_k_135, sizeof(__pyx_k_135), 0, 0, 1, 0},
+ {&__pyx_kp_s_136, __pyx_k_136, sizeof(__pyx_k_136), 0, 0, 1, 0},
+ {&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0},
+ {&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0},
+ {&__pyx_kp_s_140, __pyx_k_140, sizeof(__pyx_k_140), 0, 0, 1, 0},
+ {&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0},
+ {&__pyx_kp_s_145, __pyx_k_145, sizeof(__pyx_k_145), 0, 0, 1, 0},
+ {&__pyx_n_s_147, __pyx_k_147, sizeof(__pyx_k_147), 0, 0, 1, 1},
+ {&__pyx_kp_s_148, __pyx_k_148, sizeof(__pyx_k_148), 0, 0, 1, 0},
+ {&__pyx_kp_s_149, __pyx_k_149, sizeof(__pyx_k_149), 0, 0, 1, 0},
+ {&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
+ {&__pyx_kp_s_150, __pyx_k_150, sizeof(__pyx_k_150), 0, 0, 1, 0},
+ {&__pyx_kp_s_151, __pyx_k_151, sizeof(__pyx_k_151), 0, 0, 1, 0},
+ {&__pyx_kp_s_152, __pyx_k_152, sizeof(__pyx_k_152), 0, 0, 1, 0},
+ {&__pyx_kp_s_153, __pyx_k_153, sizeof(__pyx_k_153), 0, 0, 1, 0},
+ {&__pyx_kp_s_154, __pyx_k_154, sizeof(__pyx_k_154), 0, 0, 1, 0},
+ {&__pyx_kp_s_155, __pyx_k_155, sizeof(__pyx_k_155), 0, 0, 1, 0},
+ {&__pyx_kp_s_156, __pyx_k_156, sizeof(__pyx_k_156), 0, 0, 1, 0},
+ {&__pyx_kp_s_157, __pyx_k_157, sizeof(__pyx_k_157), 0, 0, 1, 0},
+ {&__pyx_kp_s_158, __pyx_k_158, sizeof(__pyx_k_158), 0, 0, 1, 0},
+ {&__pyx_kp_s_159, __pyx_k_159, sizeof(__pyx_k_159), 0, 0, 1, 0},
+ {&__pyx_kp_b_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 0, 0},
+ {&__pyx_kp_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 0},
+ {&__pyx_kp_s_160, __pyx_k_160, sizeof(__pyx_k_160), 0, 0, 1, 0},
+ {&__pyx_kp_s_161, __pyx_k_161, sizeof(__pyx_k_161), 0, 0, 1, 0},
+ {&__pyx_kp_s_162, __pyx_k_162, sizeof(__pyx_k_162), 0, 0, 1, 0},
+ {&__pyx_kp_s_163, __pyx_k_163, sizeof(__pyx_k_163), 0, 0, 1, 0},
+ {&__pyx_kp_s_164, __pyx_k_164, sizeof(__pyx_k_164), 0, 0, 1, 0},
+ {&__pyx_kp_s_165, __pyx_k_165, sizeof(__pyx_k_165), 0, 0, 1, 0},
+ {&__pyx_kp_s_166, __pyx_k_166, sizeof(__pyx_k_166), 0, 0, 1, 0},
+ {&__pyx_kp_s_167, __pyx_k_167, sizeof(__pyx_k_167), 0, 0, 1, 0},
+ {&__pyx_kp_s_168, __pyx_k_168, sizeof(__pyx_k_168), 0, 0, 1, 0},
+ {&__pyx_kp_s_169, __pyx_k_169, sizeof(__pyx_k_169), 0, 0, 1, 0},
+ {&__pyx_kp_s_17, __pyx_k_17, sizeof(__pyx_k_17), 0, 0, 1, 0},
+ {&__pyx_kp_s_170, __pyx_k_170, sizeof(__pyx_k_170), 0, 0, 1, 0},
+ {&__pyx_kp_s_171, __pyx_k_171, sizeof(__pyx_k_171), 0, 0, 1, 0},
+ {&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0},
+ {&__pyx_kp_s_177, __pyx_k_177, sizeof(__pyx_k_177), 0, 0, 1, 0},
+ {&__pyx_kp_s_178, __pyx_k_178, sizeof(__pyx_k_178), 0, 0, 1, 0},
+ {&__pyx_kp_s_179, __pyx_k_179, sizeof(__pyx_k_179), 0, 0, 1, 0},
+ {&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
+ {&__pyx_kp_s_185, __pyx_k_185, sizeof(__pyx_k_185), 0, 0, 1, 0},
+ {&__pyx_kp_s_186, __pyx_k_186, sizeof(__pyx_k_186), 0, 0, 1, 0},
+ {&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
+ {&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
+ {&__pyx_n_s_249, __pyx_k_249, sizeof(__pyx_k_249), 0, 0, 1, 1},
+ {&__pyx_kp_s_251, __pyx_k_251, sizeof(__pyx_k_251), 0, 0, 1, 0},
+ {&__pyx_kp_s_256, __pyx_k_256, sizeof(__pyx_k_256), 0, 0, 1, 0},
+ {&__pyx_kp_s_257, __pyx_k_257, sizeof(__pyx_k_257), 0, 0, 1, 0},
+ {&__pyx_kp_s_266, __pyx_k_266, sizeof(__pyx_k_266), 0, 0, 1, 0},
+ {&__pyx_kp_s_273, __pyx_k_273, sizeof(__pyx_k_273), 0, 0, 1, 0},
+ {&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
+ {&__pyx_kp_s_290, __pyx_k_290, sizeof(__pyx_k_290), 0, 0, 1, 0},
+ {&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
+ {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
+ {&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
+ {&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
+ {&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0},
+ {&__pyx_kp_s_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 1, 0},
+ {&__pyx_kp_s_35, __pyx_k_35, sizeof(__pyx_k_35), 0, 0, 1, 0},
+ {&__pyx_kp_s_36, __pyx_k_36, sizeof(__pyx_k_36), 0, 0, 1, 0},
+ {&__pyx_kp_b_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 0, 0},
+ {&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0},
+ {&__pyx_kp_s_41, __pyx_k_41, sizeof(__pyx_k_41), 0, 0, 1, 0},
+ {&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0},
+ {&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0},
+ {&__pyx_kp_s_46, __pyx_k_46, sizeof(__pyx_k_46), 0, 0, 1, 0},
+ {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0},
+ {&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0},
{&__pyx_kp_s_50, __pyx_k_50, sizeof(__pyx_k_50), 0, 0, 1, 0},
- {&__pyx_kp_s_51, __pyx_k_51, sizeof(__pyx_k_51), 0, 0, 1, 0},
- {&__pyx_kp_s_52, __pyx_k_52, sizeof(__pyx_k_52), 0, 0, 1, 0},
- {&__pyx_kp_s_53, __pyx_k_53, sizeof(__pyx_k_53), 0, 0, 1, 0},
- {&__pyx_kp_s_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 0},
- {&__pyx_kp_s_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 0},
{&__pyx_kp_s_56, __pyx_k_56, sizeof(__pyx_k_56), 0, 0, 1, 0},
- {&__pyx_kp_s_57, __pyx_k_57, sizeof(__pyx_k_57), 0, 0, 1, 0},
- {&__pyx_kp_s_59, __pyx_k_59, sizeof(__pyx_k_59), 0, 0, 1, 0},
+ {&__pyx_kp_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 0},
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
- {&__pyx_kp_s_61, __pyx_k_61, sizeof(__pyx_k_61), 0, 0, 1, 0},
+ {&__pyx_kp_s_60, __pyx_k_60, sizeof(__pyx_k_60), 0, 0, 1, 0},
{&__pyx_kp_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 0},
- {&__pyx_n_s_63, __pyx_k_63, sizeof(__pyx_k_63), 0, 0, 1, 1},
{&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0},
- {&__pyx_kp_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 0},
{&__pyx_kp_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 0},
- {&__pyx_kp_s_67, __pyx_k_67, sizeof(__pyx_k_67), 0, 0, 1, 0},
- {&__pyx_kp_s_68, __pyx_k_68, sizeof(__pyx_k_68), 0, 0, 1, 0},
{&__pyx_kp_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 0},
{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
{&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0},
{&__pyx_kp_s_71, __pyx_k_71, sizeof(__pyx_k_71), 0, 0, 1, 0},
- {&__pyx_kp_s_72, __pyx_k_72, sizeof(__pyx_k_72), 0, 0, 1, 0},
- {&__pyx_kp_s_73, __pyx_k_73, sizeof(__pyx_k_73), 0, 0, 1, 0},
- {&__pyx_kp_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 0},
- {&__pyx_kp_s_75, __pyx_k_75, sizeof(__pyx_k_75), 0, 0, 1, 0},
{&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0},
- {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0},
- {&__pyx_kp_s_78, __pyx_k_78, sizeof(__pyx_k_78), 0, 0, 1, 0},
{&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0},
- {&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0},
- {&__pyx_kp_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 0},
- {&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0},
{&__pyx_kp_s_82, __pyx_k_82, sizeof(__pyx_k_82), 0, 0, 1, 0},
- {&__pyx_kp_s_83, __pyx_k_83, sizeof(__pyx_k_83), 0, 0, 1, 0},
- {&__pyx_kp_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 0},
{&__pyx_kp_s_85, __pyx_k_85, sizeof(__pyx_k_85), 0, 0, 1, 0},
- {&__pyx_kp_s_86, __pyx_k_86, sizeof(__pyx_k_86), 0, 0, 1, 0},
- {&__pyx_kp_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 0},
- {&__pyx_kp_s_88, __pyx_k_88, sizeof(__pyx_k_88), 0, 0, 1, 0},
- {&__pyx_kp_s_89, __pyx_k_89, sizeof(__pyx_k_89), 0, 0, 1, 0},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
- {&__pyx_kp_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 0},
- {&__pyx_kp_s_91, __pyx_k_91, sizeof(__pyx_k_91), 0, 0, 1, 0},
{&__pyx_kp_s_92, __pyx_k_92, sizeof(__pyx_k_92), 0, 0, 1, 0},
- {&__pyx_kp_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 0},
- {&__pyx_kp_s_94, __pyx_k_94, sizeof(__pyx_k_94), 0, 0, 1, 0},
{&__pyx_kp_s_95, __pyx_k_95, sizeof(__pyx_k_95), 0, 0, 1, 0},
- {&__pyx_kp_s_96, __pyx_k_96, sizeof(__pyx_k_96), 0, 0, 1, 0},
- {&__pyx_kp_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 0},
+ {&__pyx_kp_s__2scB, __pyx_k__2scB, sizeof(__pyx_k__2scB), 0, 0, 1, 0},
+ {&__pyx_kp_s__2scH, __pyx_k__2scH, sizeof(__pyx_k__2scH), 0, 0, 1, 0},
+ {&__pyx_kp_s__2scI, __pyx_k__2scI, sizeof(__pyx_k__2scI), 0, 0, 1, 0},
+ {&__pyx_kp_s__2scb, __pyx_k__2scb, sizeof(__pyx_k__2scb), 0, 0, 1, 0},
+ {&__pyx_kp_s__2scc, __pyx_k__2scc, sizeof(__pyx_k__2scc), 0, 0, 1, 0},
+ {&__pyx_kp_s__2scf, __pyx_k__2scf, sizeof(__pyx_k__2scf), 0, 0, 1, 0},
+ {&__pyx_kp_s__2sch, __pyx_k__2sch, sizeof(__pyx_k__2sch), 0, 0, 1, 0},
+ {&__pyx_kp_s__2sci, __pyx_k__2sci, sizeof(__pyx_k__2sci), 0, 0, 1, 0},
{&__pyx_n_s__A, __pyx_k__A, sizeof(__pyx_k__A), 0, 0, 1, 1},
{&__pyx_n_s__AS, __pyx_k__AS, sizeof(__pyx_k__AS), 0, 0, 1, 1},
{&__pyx_n_s__AlignedRead, __pyx_k__AlignedRead, sizeof(__pyx_k__AlignedRead), 0, 0, 1, 1},
+ {&__pyx_n_s__AttributeError, __pyx_k__AttributeError, sizeof(__pyx_k__AttributeError), 0, 0, 1, 1},
+ {&__pyx_n_s__B, __pyx_k__B, sizeof(__pyx_k__B), 0, 0, 1, 1},
{&__pyx_n_s__C, __pyx_k__C, sizeof(__pyx_k__C), 0, 0, 1, 1},
+ {&__pyx_n_s__CIGAR2CODE, __pyx_k__CIGAR2CODE, sizeof(__pyx_k__CIGAR2CODE), 0, 0, 1, 1},
+ {&__pyx_n_s__CIGAR_REGEX, __pyx_k__CIGAR_REGEX, sizeof(__pyx_k__CIGAR_REGEX), 0, 0, 1, 1},
{&__pyx_n_s__CL, __pyx_k__CL, sizeof(__pyx_k__CL), 0, 0, 1, 1},
{&__pyx_n_s__CN, __pyx_k__CN, sizeof(__pyx_k__CN), 0, 0, 1, 1},
{&__pyx_n_s__CO, __pyx_k__CO, sizeof(__pyx_k__CO), 0, 0, 1, 1},
{&__pyx_n_s__D, __pyx_k__D, sizeof(__pyx_k__D), 0, 0, 1, 1},
{&__pyx_n_s__DS, __pyx_k__DS, sizeof(__pyx_k__DS), 0, 0, 1, 1},
{&__pyx_n_s__DT, __pyx_k__DT, sizeof(__pyx_k__DT), 0, 0, 1, 1},
- {&__pyx_n_s__DictType, __pyx_k__DictType, sizeof(__pyx_k__DictType), 0, 0, 1, 1},
{&__pyx_n_s__F, __pyx_k__F, sizeof(__pyx_k__F), 0, 0, 1, 1},
+ {&__pyx_n_s__FO, __pyx_k__FO, sizeof(__pyx_k__FO), 0, 0, 1, 1},
{&__pyx_n_s__Fastafile, __pyx_k__Fastafile, sizeof(__pyx_k__Fastafile), 0, 0, 1, 1},
- {&__pyx_n_s__FloatType, __pyx_k__FloatType, sizeof(__pyx_k__FloatType), 0, 0, 1, 1},
{&__pyx_n_s__GO, __pyx_k__GO, sizeof(__pyx_k__GO), 0, 0, 1, 1},
+ {&__pyx_n_s__H, __pyx_k__H, sizeof(__pyx_k__H), 0, 0, 1, 1},
{&__pyx_n_s__HD, __pyx_k__HD, sizeof(__pyx_k__HD), 0, 0, 1, 1},
{&__pyx_n_s__I, __pyx_k__I, sizeof(__pyx_k__I), 0, 0, 1, 1},
{&__pyx_n_s__ID, __pyx_k__ID, sizeof(__pyx_k__ID), 0, 0, 1, 1},
{&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
- {&__pyx_n_s__IndelCaller, __pyx_k__IndelCaller, sizeof(__pyx_k__IndelCaller), 0, 0, 1, 1},
+ {&__pyx_n_s__IS_PYTHON3, __pyx_k__IS_PYTHON3, sizeof(__pyx_k__IS_PYTHON3), 0, 0, 1, 1},
{&__pyx_n_s__IndexedReads, __pyx_k__IndexedReads, sizeof(__pyx_k__IndexedReads), 0, 0, 1, 1},
- {&__pyx_n_s__IntType, __pyx_k__IntType, sizeof(__pyx_k__IntType), 0, 0, 1, 1},
{&__pyx_n_s__IteratorColumn, __pyx_k__IteratorColumn, sizeof(__pyx_k__IteratorColumn), 0, 0, 1, 1},
- {&__pyx_n_s__IteratorIndelCalls, __pyx_k__IteratorIndelCalls, sizeof(__pyx_k__IteratorIndelCalls), 0, 0, 1, 1},
{&__pyx_n_s__IteratorRow, __pyx_k__IteratorRow, sizeof(__pyx_k__IteratorRow), 0, 0, 1, 1},
- {&__pyx_n_s__IteratorRowAll, __pyx_k__IteratorRowAll, sizeof(__pyx_k__IteratorRowAll), 0, 0, 1, 1},
- {&__pyx_n_s__IteratorRowAllRefs, __pyx_k__IteratorRowAllRefs, sizeof(__pyx_k__IteratorRowAllRefs), 0, 0, 1, 1},
- {&__pyx_n_s__IteratorRowRegion, __pyx_k__IteratorRowRegion, sizeof(__pyx_k__IteratorRowRegion), 0, 0, 1, 1},
- {&__pyx_n_s__IteratorSNPCalls, __pyx_k__IteratorSNPCalls, sizeof(__pyx_k__IteratorSNPCalls), 0, 0, 1, 1},
+ {&__pyx_n_s__KS, __pyx_k__KS, sizeof(__pyx_k__KS), 0, 0, 1, 1},
{&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
{&__pyx_n_s__LB, __pyx_k__LB, sizeof(__pyx_k__LB), 0, 0, 1, 1},
{&__pyx_n_s__LN, __pyx_k__LN, sizeof(__pyx_k__LN), 0, 0, 1, 1},
{&__pyx_n_s__M5, __pyx_k__M5, sizeof(__pyx_k__M5), 0, 0, 1, 1},
{&__pyx_n_s__NotImplementedError, __pyx_k__NotImplementedError, sizeof(__pyx_k__NotImplementedError), 0, 0, 1, 1},
+ {&__pyx_n_s__OSError, __pyx_k__OSError, sizeof(__pyx_k__OSError), 0, 0, 1, 1},
{&__pyx_n_s__O_CREAT, __pyx_k__O_CREAT, sizeof(__pyx_k__O_CREAT), 0, 0, 1, 1},
{&__pyx_n_s__O_WRONLY, __pyx_k__O_WRONLY, sizeof(__pyx_k__O_WRONLY), 0, 0, 1, 1},
{&__pyx_n_s__Outs, __pyx_k__Outs, sizeof(__pyx_k__Outs), 0, 0, 1, 1},
{&__pyx_n_s__S, __pyx_k__S, sizeof(__pyx_k__S), 0, 0, 1, 1},
{&__pyx_n_s__SM, __pyx_k__SM, sizeof(__pyx_k__SM), 0, 0, 1, 1},
{&__pyx_n_s__SN, __pyx_k__SN, sizeof(__pyx_k__SN), 0, 0, 1, 1},
- {&__pyx_n_s__SNPCaller, __pyx_k__SNPCaller, sizeof(__pyx_k__SNPCaller), 0, 0, 1, 1},
{&__pyx_n_s__SO, __pyx_k__SO, sizeof(__pyx_k__SO), 0, 0, 1, 1},
{&__pyx_n_s__SP, __pyx_k__SP, sizeof(__pyx_k__SP), 0, 0, 1, 1},
{&__pyx_n_s__SQ, __pyx_k__SQ, sizeof(__pyx_k__SQ), 0, 0, 1, 1},
{&__pyx_n_s__StopIteration, __pyx_k__StopIteration, sizeof(__pyx_k__StopIteration), 0, 0, 1, 1},
{&__pyx_n_s__TypeError, __pyx_k__TypeError, sizeof(__pyx_k__TypeError), 0, 0, 1, 1},
{&__pyx_n_s__UR, __pyx_k__UR, sizeof(__pyx_k__UR), 0, 0, 1, 1},
+ {&__pyx_n_s__UnicodeDecodeError, __pyx_k__UnicodeDecodeError, sizeof(__pyx_k__UnicodeDecodeError), 0, 0, 1, 1},
{&__pyx_n_s__VALID_HEADERS, __pyx_k__VALID_HEADERS, sizeof(__pyx_k__VALID_HEADERS), 0, 0, 1, 1},
{&__pyx_n_s__VALID_HEADER_FIELDS, __pyx_k__VALID_HEADER_FIELDS, sizeof(__pyx_k__VALID_HEADER_FIELDS), 0, 0, 1, 1},
{&__pyx_n_s__VALID_HEADER_ORDER, __pyx_k__VALID_HEADER_ORDER, sizeof(__pyx_k__VALID_HEADER_ORDER), 0, 0, 1, 1},
{&__pyx_n_s____all__, __pyx_k____all__, sizeof(__pyx_k____all__), 0, 0, 1, 1},
{&__pyx_n_s____del__, __pyx_k____del__, sizeof(__pyx_k____del__), 0, 0, 1, 1},
{&__pyx_n_s____dict__, __pyx_k____dict__, sizeof(__pyx_k____dict__), 0, 0, 1, 1},
+ {&__pyx_n_s____enter__, __pyx_k____enter__, sizeof(__pyx_k____enter__), 0, 0, 1, 1},
+ {&__pyx_n_s____exit__, __pyx_k____exit__, sizeof(__pyx_k____exit__), 0, 0, 1, 1},
{&__pyx_n_s____getattribute__, __pyx_k____getattribute__, sizeof(__pyx_k____getattribute__), 0, 0, 1, 1},
{&__pyx_n_s____init__, __pyx_k____init__, sizeof(__pyx_k____init__), 0, 0, 1, 1},
{&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1},
- {&__pyx_n_s____next__, __pyx_k____next__, sizeof(__pyx_k____next__), 0, 0, 1, 1},
{&__pyx_n_s____str__, __pyx_k____str__, sizeof(__pyx_k____str__), 0, 0, 1, 1},
{&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1},
- {&__pyx_n_s___alignment, __pyx_k___alignment, sizeof(__pyx_k___alignment), 0, 0, 1, 1},
- {&__pyx_n_s___buildHeader, __pyx_k___buildHeader, sizeof(__pyx_k___buildHeader), 0, 0, 1, 1},
{&__pyx_n_s___buildLine, __pyx_k___buildLine, sizeof(__pyx_k___buildLine), 0, 0, 1, 1},
- {&__pyx_n_s___call, __pyx_k___call, sizeof(__pyx_k___call), 0, 0, 1, 1},
- {&__pyx_n_s___consensus_quality, __pyx_k___consensus_quality, sizeof(__pyx_k___consensus_quality), 0, 0, 1, 1},
- {&__pyx_n_s___coverage, __pyx_k___coverage, sizeof(__pyx_k___coverage), 0, 0, 1, 1},
- {&__pyx_n_s___delegate, __pyx_k___delegate, sizeof(__pyx_k___delegate), 0, 0, 1, 1},
- {&__pyx_n_s___filename, __pyx_k___filename, sizeof(__pyx_k___filename), 0, 0, 1, 1},
- {&__pyx_n_s___genotype, __pyx_k___genotype, sizeof(__pyx_k___genotype), 0, 0, 1, 1},
{&__pyx_n_s___hasIndex, __pyx_k___hasIndex, sizeof(__pyx_k___hasIndex), 0, 0, 1, 1},
- {&__pyx_n_s___indel, __pyx_k___indel, sizeof(__pyx_k___indel), 0, 0, 1, 1},
{&__pyx_n_s___isOpen, __pyx_k___isOpen, sizeof(__pyx_k___isOpen), 0, 0, 1, 1},
- {&__pyx_n_s___is_del, __pyx_k___is_del, sizeof(__pyx_k___is_del), 0, 0, 1, 1},
- {&__pyx_n_s___is_head, __pyx_k___is_head, sizeof(__pyx_k___is_head), 0, 0, 1, 1},
- {&__pyx_n_s___is_tail, __pyx_k___is_tail, sizeof(__pyx_k___is_tail), 0, 0, 1, 1},
- {&__pyx_n_s___level, __pyx_k___level, sizeof(__pyx_k___level), 0, 0, 1, 1},
- {&__pyx_n_s___logfile, __pyx_k___logfile, sizeof(__pyx_k___logfile), 0, 0, 1, 1},
{&__pyx_n_s___open, __pyx_k___open, sizeof(__pyx_k___open), 0, 0, 1, 1},
{&__pyx_n_s___parseRegion, __pyx_k___parseRegion, sizeof(__pyx_k___parseRegion), 0, 0, 1, 1},
- {&__pyx_n_s___pos, __pyx_k___pos, sizeof(__pyx_k___pos), 0, 0, 1, 1},
- {&__pyx_n_s___qpos, __pyx_k___qpos, sizeof(__pyx_k___qpos), 0, 0, 1, 1},
- {&__pyx_n_s___r, __pyx_k___r, sizeof(__pyx_k___r), 0, 0, 1, 1},
- {&__pyx_n_s___reference_base, __pyx_k___reference_base, sizeof(__pyx_k___reference_base), 0, 0, 1, 1},
{&__pyx_n_s___samtools_dispatch, __pyx_k___samtools_dispatch, sizeof(__pyx_k___samtools_dispatch), 0, 0, 1, 1},
- {&__pyx_n_s___snp_quality, __pyx_k___snp_quality, sizeof(__pyx_k___snp_quality), 0, 0, 1, 1},
- {&__pyx_n_s___tid, __pyx_k___tid, sizeof(__pyx_k___tid), 0, 0, 1, 1},
- {&__pyx_n_s__addReference, __pyx_k__addReference, sizeof(__pyx_k__addReference), 0, 0, 1, 1},
+ {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1},
+ {&__pyx_n_s__add_sq_text, __pyx_k__add_sq_text, sizeof(__pyx_k__add_sq_text), 0, 0, 1, 1},
{&__pyx_n_s__alignment, __pyx_k__alignment, sizeof(__pyx_k__alignment), 0, 0, 1, 1},
{&__pyx_n_s__all, __pyx_k__all, sizeof(__pyx_k__all), 0, 0, 1, 1},
{&__pyx_n_s__args, __pyx_k__args, sizeof(__pyx_k__args), 0, 0, 1, 1},
+ {&__pyx_n_s__ascii, __pyx_k__ascii, sizeof(__pyx_k__ascii), 0, 0, 1, 1},
{&__pyx_n_s__b, __pyx_k__b, sizeof(__pyx_k__b), 0, 0, 1, 1},
- {&__pyx_n_s__bam, __pyx_k__bam, sizeof(__pyx_k__bam), 0, 0, 1, 1},
{&__pyx_n_s__beg, __pyx_k__beg, sizeof(__pyx_k__beg), 0, 0, 1, 1},
{&__pyx_n_s__bin, __pyx_k__bin, sizeof(__pyx_k__bin), 0, 0, 1, 1},
{&__pyx_n_s__bqual, __pyx_k__bqual, sizeof(__pyx_k__bqual), 0, 0, 1, 1},
- {&__pyx_n_s__build, __pyx_k__build, sizeof(__pyx_k__build), 0, 0, 1, 1},
{&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1},
{&__pyx_n_s__calcsize, __pyx_k__calcsize, sizeof(__pyx_k__calcsize), 0, 0, 1, 1},
- {&__pyx_n_s__call, __pyx_k__call, sizeof(__pyx_k__call), 0, 0, 1, 1},
{&__pyx_n_s__callback, __pyx_k__callback, sizeof(__pyx_k__callback), 0, 0, 1, 1},
- {&__pyx_n_s__cap_mapQ, __pyx_k__cap_mapQ, sizeof(__pyx_k__cap_mapQ), 0, 0, 1, 1},
- {&__pyx_n_s__catch_stderr, __pyx_k__catch_stderr, sizeof(__pyx_k__catch_stderr), 0, 0, 1, 1},
+ {&__pyx_n_s__cargs, __pyx_k__cargs, sizeof(__pyx_k__cargs), 0, 0, 1, 1},
{&__pyx_n_s__catch_stdout, __pyx_k__catch_stdout, sizeof(__pyx_k__catch_stdout), 0, 0, 1, 1},
+ {&__pyx_n_s__check_header, __pyx_k__check_header, sizeof(__pyx_k__check_header), 0, 0, 1, 1},
+ {&__pyx_n_s__check_sq, __pyx_k__check_sq, sizeof(__pyx_k__check_sq), 0, 0, 1, 1},
{&__pyx_n_s__chr, __pyx_k__chr, sizeof(__pyx_k__chr), 0, 0, 1, 1},
{&__pyx_n_s__cigar, __pyx_k__cigar, sizeof(__pyx_k__cigar), 0, 0, 1, 1},
{&__pyx_n_s__close, __pyx_k__close, sizeof(__pyx_k__close), 0, 0, 1, 1},
- {&__pyx_n_s__cmp, __pyx_k__cmp, sizeof(__pyx_k__cmp), 0, 0, 1, 1},
- {&__pyx_n_s__cnext, __pyx_k__cnext, sizeof(__pyx_k__cnext), 0, 0, 1, 1},
- {&__pyx_n_s__cnt1, __pyx_k__cnt1, sizeof(__pyx_k__cnt1), 0, 0, 1, 1},
- {&__pyx_n_s__cnt2, __pyx_k__cnt2, sizeof(__pyx_k__cnt2), 0, 0, 1, 1},
- {&__pyx_n_s__cnt_anti, __pyx_k__cnt_anti, sizeof(__pyx_k__cnt_anti), 0, 0, 1, 1},
{&__pyx_n_s__collections, __pyx_k__collections, sizeof(__pyx_k__collections), 0, 0, 1, 1},
- {&__pyx_n_s__compare, __pyx_k__compare, sizeof(__pyx_k__compare), 0, 0, 1, 1},
+ {&__pyx_n_s__compile, __pyx_k__compile, sizeof(__pyx_k__compile), 0, 0, 1, 1},
{&__pyx_n_s__consensus_quality, __pyx_k__consensus_quality, sizeof(__pyx_k__consensus_quality), 0, 0, 1, 1},
- {&__pyx_n_s__core, __pyx_k__core, sizeof(__pyx_k__core), 0, 0, 1, 1},
- {&__pyx_n_s__count, __pyx_k__count, sizeof(__pyx_k__count), 0, 0, 1, 1},
{&__pyx_n_s__coverage, __pyx_k__coverage, sizeof(__pyx_k__coverage), 0, 0, 1, 1},
+ {&__pyx_n_s__csamtools, __pyx_k__csamtools, sizeof(__pyx_k__csamtools), 0, 0, 1, 1},
{&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1},
- {&__pyx_n_s__current_pos, __pyx_k__current_pos, sizeof(__pyx_k__current_pos), 0, 0, 1, 1},
{&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1},
- {&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1},
{&__pyx_n_s__data_len, __pyx_k__data_len, sizeof(__pyx_k__data_len), 0, 0, 1, 1},
+ {&__pyx_n_s__decode, __pyx_k__decode, sizeof(__pyx_k__decode), 0, 0, 1, 1},
{&__pyx_n_s__defaultdict, __pyx_k__defaultdict, sizeof(__pyx_k__defaultdict), 0, 0, 1, 1},
- {&__pyx_n_s__devnull, __pyx_k__devnull, sizeof(__pyx_k__devnull), 0, 0, 1, 1},
{&__pyx_n_s__dup, __pyx_k__dup, sizeof(__pyx_k__dup), 0, 0, 1, 1},
{&__pyx_n_s__dup2, __pyx_k__dup2, sizeof(__pyx_k__dup2), 0, 0, 1, 1},
+ {&__pyx_n_s__encode, __pyx_k__encode, sizeof(__pyx_k__encode), 0, 0, 1, 1},
{&__pyx_n_s__end, __pyx_k__end, sizeof(__pyx_k__end), 0, 0, 1, 1},
- {&__pyx_n_s__errmod, __pyx_k__errmod, sizeof(__pyx_k__errmod), 0, 0, 1, 1},
+ {&__pyx_n_s__enumerate, __pyx_k__enumerate, sizeof(__pyx_k__enumerate), 0, 0, 1, 1},
{&__pyx_n_s__exc_type, __pyx_k__exc_type, sizeof(__pyx_k__exc_type), 0, 0, 1, 1},
{&__pyx_n_s__exc_value, __pyx_k__exc_value, sizeof(__pyx_k__exc_value), 0, 0, 1, 1},
{&__pyx_n_s__exists, __pyx_k__exists, sizeof(__pyx_k__exists), 0, 0, 1, 1},
+ {&__pyx_n_s__extend, __pyx_k__extend, sizeof(__pyx_k__extend), 0, 0, 1, 1},
{&__pyx_n_s__f, __pyx_k__f, sizeof(__pyx_k__f), 0, 0, 1, 1},
- {&__pyx_n_s__fancy_str, __pyx_k__fancy_str, sizeof(__pyx_k__fancy_str), 0, 0, 1, 1},
{&__pyx_n_s__fastafile, __pyx_k__fastafile, sizeof(__pyx_k__fastafile), 0, 0, 1, 1},
{&__pyx_n_s__fd, __pyx_k__fd, sizeof(__pyx_k__fd), 0, 0, 1, 1},
- {&__pyx_n_s__fetch, __pyx_k__fetch, sizeof(__pyx_k__fetch), 0, 0, 1, 1},
{&__pyx_n_s__fields, __pyx_k__fields, sizeof(__pyx_k__fields), 0, 0, 1, 1},
{&__pyx_n_s__filename, __pyx_k__filename, sizeof(__pyx_k__filename), 0, 0, 1, 1},
{&__pyx_n_s__fileno, __pyx_k__fileno, sizeof(__pyx_k__fileno), 0, 0, 1, 1},
- {&__pyx_n_s__first_allele, __pyx_k__first_allele, sizeof(__pyx_k__first_allele), 0, 0, 1, 1},
+ {&__pyx_n_s__findall, __pyx_k__findall, sizeof(__pyx_k__findall), 0, 0, 1, 1},
{&__pyx_n_s__flag, __pyx_k__flag, sizeof(__pyx_k__flag), 0, 0, 1, 1},
{&__pyx_n_s__flush, __pyx_k__flush, sizeof(__pyx_k__flush), 0, 0, 1, 1},
- {&__pyx_n_s__fp, __pyx_k__fp, sizeof(__pyx_k__fp), 0, 0, 1, 1},
{&__pyx_n_s__genotype, __pyx_k__genotype, sizeof(__pyx_k__genotype), 0, 0, 1, 1},
- {&__pyx_n_s__getSequence, __pyx_k__getSequence, sizeof(__pyx_k__getSequence), 0, 0, 1, 1},
- {&__pyx_n_s__getrname, __pyx_k__getrname, sizeof(__pyx_k__getrname), 0, 0, 1, 1},
+ {&__pyx_n_s__getdefaultencoding, __pyx_k__getdefaultencoding, sizeof(__pyx_k__getdefaultencoding), 0, 0, 1, 1},
{&__pyx_n_s__gettid, __pyx_k__gettid, sizeof(__pyx_k__gettid), 0, 0, 1, 1},
- {&__pyx_n_s__hasReference, __pyx_k__hasReference, sizeof(__pyx_k__hasReference), 0, 0, 1, 1},
- {&__pyx_n_s__hash, __pyx_k__hash, sizeof(__pyx_k__hash), 0, 0, 1, 1},
+ {&__pyx_n_s__h, __pyx_k__h, sizeof(__pyx_k__h), 0, 0, 1, 1},
{&__pyx_n_s__header, __pyx_k__header, sizeof(__pyx_k__header), 0, 0, 1, 1},
- {&__pyx_n_s__het_rate, __pyx_k__het_rate, sizeof(__pyx_k__het_rate), 0, 0, 1, 1},
{&__pyx_n_s__i, __pyx_k__i, sizeof(__pyx_k__i), 0, 0, 1, 1},
{&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1},
{&__pyx_n_s__indel, __pyx_k__indel, sizeof(__pyx_k__indel), 0, 0, 1, 1},
- {&__pyx_n_s__indel1, __pyx_k__indel1, sizeof(__pyx_k__indel1), 0, 0, 1, 1},
- {&__pyx_n_s__indel2, __pyx_k__indel2, sizeof(__pyx_k__indel2), 0, 0, 1, 1},
{&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1},
+ {&__pyx_n_s__inf, __pyx_k__inf, sizeof(__pyx_k__inf), 0, 0, 1, 1},
{&__pyx_n_s__is_del, __pyx_k__is_del, sizeof(__pyx_k__is_del), 0, 0, 1, 1},
{&__pyx_n_s__is_head, __pyx_k__is_head, sizeof(__pyx_k__is_head), 0, 0, 1, 1},
{&__pyx_n_s__is_tail, __pyx_k__is_tail, sizeof(__pyx_k__is_tail), 0, 0, 1, 1},
- {&__pyx_n_s__isbam, __pyx_k__isbam, sizeof(__pyx_k__isbam), 0, 0, 1, 1},
{&__pyx_n_s__isize, __pyx_k__isize, sizeof(__pyx_k__isize), 0, 0, 1, 1},
- {&__pyx_n_s__isremote, __pyx_k__isremote, sizeof(__pyx_k__isremote), 0, 0, 1, 1},
+ {&__pyx_n_s__islower, __pyx_k__islower, sizeof(__pyx_k__islower), 0, 0, 1, 1},
{&__pyx_n_s__isupper, __pyx_k__isupper, sizeof(__pyx_k__isupper), 0, 0, 1, 1},
- {&__pyx_n_s__iter, __pyx_k__iter, sizeof(__pyx_k__iter), 0, 0, 1, 1},
- {&__pyx_n_s__iterator_column, __pyx_k__iterator_column, sizeof(__pyx_k__iterator_column), 0, 0, 1, 1},
- {&__pyx_n_s__iterdata, __pyx_k__iterdata, sizeof(__pyx_k__iterdata), 0, 0, 1, 1},
+ {&__pyx_n_s__items, __pyx_k__items, sizeof(__pyx_k__items), 0, 0, 1, 1},
{&__pyx_n_s__itertools, __pyx_k__itertools, sizeof(__pyx_k__itertools), 0, 0, 1, 1},
{&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1},
{&__pyx_n_s__l_aux, __pyx_k__l_aux, sizeof(__pyx_k__l_aux), 0, 0, 1, 1},
{&__pyx_n_s__l_qname, __pyx_k__l_qname, sizeof(__pyx_k__l_qname), 0, 0, 1, 1},
{&__pyx_n_s__l_qseq, __pyx_k__l_qseq, sizeof(__pyx_k__l_qseq), 0, 0, 1, 1},
- {&__pyx_n_s__l_text, __pyx_k__l_text, sizeof(__pyx_k__l_text), 0, 0, 1, 1},
+ {&__pyx_n_s__lengths, __pyx_k__lengths, sizeof(__pyx_k__lengths), 0, 0, 1, 1},
{&__pyx_n_s__level, __pyx_k__level, sizeof(__pyx_k__level), 0, 0, 1, 1},
{&__pyx_n_s__m_data, __pyx_k__m_data, sizeof(__pyx_k__m_data), 0, 0, 1, 1},
{&__pyx_n_s__map, __pyx_k__map, sizeof(__pyx_k__map), 0, 0, 1, 1},
{&__pyx_n_s__mapping_quality, __pyx_k__mapping_quality, sizeof(__pyx_k__mapping_quality), 0, 0, 1, 1},
{&__pyx_n_s__mapq, __pyx_k__mapq, sizeof(__pyx_k__mapq), 0, 0, 1, 1},
{&__pyx_n_s__mask, __pyx_k__mask, sizeof(__pyx_k__mask), 0, 0, 1, 1},
- {&__pyx_n_s__mate, __pyx_k__mate, sizeof(__pyx_k__mate), 0, 0, 1, 1},
+ {&__pyx_n_s__max, __pyx_k__max, sizeof(__pyx_k__max), 0, 0, 1, 1},
{&__pyx_n_s__max_depth, __pyx_k__max_depth, sizeof(__pyx_k__max_depth), 0, 0, 1, 1},
{&__pyx_n_s__method, __pyx_k__method, sizeof(__pyx_k__method), 0, 0, 1, 1},
- {&__pyx_n_s__min_baseQ, __pyx_k__min_baseQ, sizeof(__pyx_k__min_baseQ), 0, 0, 1, 1},
+ {&__pyx_n_s__min, __pyx_k__min, sizeof(__pyx_k__min), 0, 0, 1, 1},
{&__pyx_n_s__mkstemp, __pyx_k__mkstemp, sizeof(__pyx_k__mkstemp), 0, 0, 1, 1},
{&__pyx_n_s__mode, __pyx_k__mode, sizeof(__pyx_k__mode), 0, 0, 1, 1},
{&__pyx_n_s__mpos, __pyx_k__mpos, sizeof(__pyx_k__mpos), 0, 0, 1, 1},
{&__pyx_n_s__mtid, __pyx_k__mtid, sizeof(__pyx_k__mtid), 0, 0, 1, 1},
{&__pyx_n_s__n, __pyx_k__n, sizeof(__pyx_k__n), 0, 0, 1, 1},
{&__pyx_n_s__n_cigar, __pyx_k__n_cigar, sizeof(__pyx_k__n_cigar), 0, 0, 1, 1},
- {&__pyx_n_s__n_hap, __pyx_k__n_hap, sizeof(__pyx_k__n_hap), 0, 0, 1, 1},
- {&__pyx_n_s__n_haplotypes, __pyx_k__n_haplotypes, sizeof(__pyx_k__n_haplotypes), 0, 0, 1, 1},
- {&__pyx_n_s__n_plp, __pyx_k__n_plp, sizeof(__pyx_k__n_plp), 0, 0, 1, 1},
- {&__pyx_n_s__n_pu, __pyx_k__n_pu, sizeof(__pyx_k__n_pu), 0, 0, 1, 1},
- {&__pyx_n_s__n_targets, __pyx_k__n_targets, sizeof(__pyx_k__n_targets), 0, 0, 1, 1},
- {&__pyx_n_s__name, __pyx_k__name, sizeof(__pyx_k__name), 0, 0, 1, 1},
{&__pyx_n_s__nextiter, __pyx_k__nextiter, sizeof(__pyx_k__nextiter), 0, 0, 1, 1},
{&__pyx_n_s__nreferences, __pyx_k__nreferences, sizeof(__pyx_k__nreferences), 0, 0, 1, 1},
{&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1},
+ {&__pyx_n_s__ofd, __pyx_k__ofd, sizeof(__pyx_k__ofd), 0, 0, 1, 1},
{&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1},
{&__pyx_n_s__open, __pyx_k__open, sizeof(__pyx_k__open), 0, 0, 1, 1},
- {&__pyx_n_s__opt, __pyx_k__opt, sizeof(__pyx_k__opt), 0, 0, 1, 1},
- {&__pyx_n_s__options, __pyx_k__options, sizeof(__pyx_k__options), 0, 0, 1, 1},
+ {&__pyx_n_s__ord, __pyx_k__ord, sizeof(__pyx_k__ord), 0, 0, 1, 1},
{&__pyx_n_s__os, __pyx_k__os, sizeof(__pyx_k__os), 0, 0, 1, 1},
- {&__pyx_n_s__overlap, __pyx_k__overlap, sizeof(__pyx_k__overlap), 0, 0, 1, 1},
- {&__pyx_n_s__owns_samfile, __pyx_k__owns_samfile, sizeof(__pyx_k__owns_samfile), 0, 0, 1, 1},
+ {&__pyx_n_s__out_stderr, __pyx_k__out_stderr, sizeof(__pyx_k__out_stderr), 0, 0, 1, 1},
+ {&__pyx_n_s__out_stdout, __pyx_k__out_stdout, sizeof(__pyx_k__out_stdout), 0, 0, 1, 1},
{&__pyx_n_s__pack_into, __pyx_k__pack_into, sizeof(__pyx_k__pack_into), 0, 0, 1, 1},
{&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1},
- {&__pyx_n_s__pileup, __pyx_k__pileup, sizeof(__pyx_k__pileup), 0, 0, 1, 1},
- {&__pyx_n_s__pileup_iter, __pyx_k__pileup_iter, sizeof(__pyx_k__pileup_iter), 0, 0, 1, 1},
{&__pyx_n_s__pileups, __pyx_k__pileups, sizeof(__pyx_k__pileups), 0, 0, 1, 1},
{&__pyx_n_s__platform, __pyx_k__platform, sizeof(__pyx_k__platform), 0, 0, 1, 1},
- {&__pyx_n_s__plp, __pyx_k__plp, sizeof(__pyx_k__plp), 0, 0, 1, 1},
{&__pyx_n_s__port, __pyx_k__port, sizeof(__pyx_k__port), 0, 0, 1, 1},
{&__pyx_n_s__pos, __pyx_k__pos, sizeof(__pyx_k__pos), 0, 0, 1, 1},
{&__pyx_n_s__positions, __pyx_k__positions, sizeof(__pyx_k__positions), 0, 0, 1, 1},
- {&__pyx_n_s__q_cns, __pyx_k__q_cns, sizeof(__pyx_k__q_cns), 0, 0, 1, 1},
- {&__pyx_n_s__q_indel, __pyx_k__q_indel, sizeof(__pyx_k__q_indel), 0, 0, 1, 1},
- {&__pyx_n_s__q_r, __pyx_k__q_r, sizeof(__pyx_k__q_r), 0, 0, 1, 1},
- {&__pyx_n_s__q_ref, __pyx_k__q_ref, sizeof(__pyx_k__q_ref), 0, 0, 1, 1},
{&__pyx_n_s__qname, __pyx_k__qname, sizeof(__pyx_k__qname), 0, 0, 1, 1},
{&__pyx_n_s__qpos, __pyx_k__qpos, sizeof(__pyx_k__qpos), 0, 0, 1, 1},
{&__pyx_n_s__qseq, __pyx_k__qseq, sizeof(__pyx_k__qseq), 0, 0, 1, 1},
{&__pyx_n_s__qual, __pyx_k__qual, sizeof(__pyx_k__qual), 0, 0, 1, 1},
+ {&__pyx_n_b__r, __pyx_k__r, sizeof(__pyx_k__r), 0, 0, 0, 1},
{&__pyx_n_s__r, __pyx_k__r, sizeof(__pyx_k__r), 0, 0, 1, 1},
- {&__pyx_n_s__r_indel, __pyx_k__r_indel, sizeof(__pyx_k__r_indel), 0, 0, 1, 1},
- {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1},
+ {&__pyx_n_s__rU, __pyx_k__rU, sizeof(__pyx_k__rU), 0, 0, 1, 1},
{&__pyx_n_s__raw, __pyx_k__raw, sizeof(__pyx_k__raw), 0, 0, 1, 1},
+ {&__pyx_n_b__rb, __pyx_k__rb, sizeof(__pyx_k__rb), 0, 0, 0, 1},
{&__pyx_n_s__rb, __pyx_k__rb, sizeof(__pyx_k__rb), 0, 0, 1, 1},
{&__pyx_n_s__re, __pyx_k__re, sizeof(__pyx_k__re), 0, 0, 1, 1},
+ {&__pyx_n_s__read, __pyx_k__read, sizeof(__pyx_k__read), 0, 0, 1, 1},
{&__pyx_n_s__readAndRelease, __pyx_k__readAndRelease, sizeof(__pyx_k__readAndRelease), 0, 0, 1, 1},
{&__pyx_n_s__readlines, __pyx_k__readlines, sizeof(__pyx_k__readlines), 0, 0, 1, 1},
- {&__pyx_n_s__reads_diff, __pyx_k__reads_diff, sizeof(__pyx_k__reads_diff), 0, 0, 1, 1},
- {&__pyx_n_s__reads_first, __pyx_k__reads_first, sizeof(__pyx_k__reads_first), 0, 0, 1, 1},
- {&__pyx_n_s__reads_second, __pyx_k__reads_second, sizeof(__pyx_k__reads_second), 0, 0, 1, 1},
{&__pyx_n_s__record, __pyx_k__record, sizeof(__pyx_k__record), 0, 0, 1, 1},
{&__pyx_n_s__reference, __pyx_k__reference, sizeof(__pyx_k__reference), 0, 0, 1, 1},
{&__pyx_n_s__reference_base, __pyx_k__reference_base, sizeof(__pyx_k__reference_base), 0, 0, 1, 1},
{&__pyx_n_s__referencelengths, __pyx_k__referencelengths, sizeof(__pyx_k__referencelengths), 0, 0, 1, 1},
{&__pyx_n_s__referencenames, __pyx_k__referencenames, sizeof(__pyx_k__referencenames), 0, 0, 1, 1},
+ {&__pyx_n_s__references, __pyx_k__references, sizeof(__pyx_k__references), 0, 0, 1, 1},
{&__pyx_n_s__region, __pyx_k__region, sizeof(__pyx_k__region), 0, 0, 1, 1},
{&__pyx_n_s__release, __pyx_k__release, sizeof(__pyx_k__release), 0, 0, 1, 1},
{&__pyx_n_s__remove, __pyx_k__remove, sizeof(__pyx_k__remove), 0, 0, 1, 1},
{&__pyx_n_s__reopen, __pyx_k__reopen, sizeof(__pyx_k__reopen), 0, 0, 1, 1},
- {&__pyx_n_s__reset, __pyx_k__reset, sizeof(__pyx_k__reset), 0, 0, 1, 1},
{&__pyx_n_s__restore, __pyx_k__restore, sizeof(__pyx_k__restore), 0, 0, 1, 1},
{&__pyx_n_s__retval, __pyx_k__retval, sizeof(__pyx_k__retval), 0, 0, 1, 1},
- {&__pyx_n_s__rg2lib, __pyx_k__rg2lib, sizeof(__pyx_k__rg2lib), 0, 0, 1, 1},
{&__pyx_n_s__rlen, __pyx_k__rlen, sizeof(__pyx_k__rlen), 0, 0, 1, 1},
{&__pyx_n_s__rname, __pyx_k__rname, sizeof(__pyx_k__rname), 0, 0, 1, 1},
- {&__pyx_n_s__rowiter, __pyx_k__rowiter, sizeof(__pyx_k__rowiter), 0, 0, 1, 1},
{&__pyx_n_s__s, __pyx_k__s, sizeof(__pyx_k__s), 0, 0, 1, 1},
{&__pyx_n_s__samfile, __pyx_k__samfile, sizeof(__pyx_k__samfile), 0, 0, 1, 1},
{&__pyx_n_s__samtools, __pyx_k__samtools, sizeof(__pyx_k__samtools), 0, 0, 1, 1},
- {&__pyx_n_s__second_allele, __pyx_k__second_allele, sizeof(__pyx_k__second_allele), 0, 0, 1, 1},
{&__pyx_n_s__seek, __pyx_k__seek, sizeof(__pyx_k__seek), 0, 0, 1, 1},
{&__pyx_n_s__self, __pyx_k__self, sizeof(__pyx_k__self), 0, 0, 1, 1},
{&__pyx_n_s__seq, __pyx_k__seq, sizeof(__pyx_k__seq), 0, 0, 1, 1},
- {&__pyx_n_s__seq_len, __pyx_k__seq_len, sizeof(__pyx_k__seq_len), 0, 0, 1, 1},
{&__pyx_n_s__setdevice, __pyx_k__setdevice, sizeof(__pyx_k__setdevice), 0, 0, 1, 1},
{&__pyx_n_s__setfd, __pyx_k__setfd, sizeof(__pyx_k__setfd), 0, 0, 1, 1},
{&__pyx_n_s__setfile, __pyx_k__setfile, sizeof(__pyx_k__setfile), 0, 0, 1, 1},
- {&__pyx_n_s__setupIteratorData, __pyx_k__setupIteratorData, sizeof(__pyx_k__setupIteratorData), 0, 0, 1, 1},
{&__pyx_n_s__snp_quality, __pyx_k__snp_quality, sizeof(__pyx_k__snp_quality), 0, 0, 1, 1},
+ {&__pyx_n_s__sorted, __pyx_k__sorted, sizeof(__pyx_k__sorted), 0, 0, 1, 1},
{&__pyx_n_s__split, __pyx_k__split, sizeof(__pyx_k__split), 0, 0, 1, 1},
{&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1},
{&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
{&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1},
{&__pyx_n_s__stderr_f, __pyx_k__stderr_f, sizeof(__pyx_k__stderr_f), 0, 0, 1, 1},
{&__pyx_n_s__stderr_h, __pyx_k__stderr_h, sizeof(__pyx_k__stderr_h), 0, 0, 1, 1},
- {&__pyx_n_s__stderr_save, __pyx_k__stderr_save, sizeof(__pyx_k__stderr_save), 0, 0, 1, 1},
{&__pyx_n_s__stdout, __pyx_k__stdout, sizeof(__pyx_k__stdout), 0, 0, 1, 1},
+ {&__pyx_n_s__stdout_f, __pyx_k__stdout_f, sizeof(__pyx_k__stdout_f), 0, 0, 1, 1},
+ {&__pyx_n_s__stdout_h, __pyx_k__stdout_h, sizeof(__pyx_k__stdout_h), 0, 0, 1, 1},
+ {&__pyx_n_s__stdout_save, __pyx_k__stdout_save, sizeof(__pyx_k__stdout_save), 0, 0, 1, 1},
{&__pyx_n_s__stepper, __pyx_k__stepper, sizeof(__pyx_k__stepper), 0, 0, 1, 1},
{&__pyx_n_s__streams, __pyx_k__streams, sizeof(__pyx_k__streams), 0, 0, 1, 1},
{&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1},
{&__pyx_n_s__sys, __pyx_k__sys, sizeof(__pyx_k__sys), 0, 0, 1, 1},
{&__pyx_n_s__system, __pyx_k__system, sizeof(__pyx_k__system), 0, 0, 1, 1},
{&__pyx_n_s__tags, __pyx_k__tags, sizeof(__pyx_k__tags), 0, 0, 1, 1},
- {&__pyx_n_s__target_len, __pyx_k__target_len, sizeof(__pyx_k__target_len), 0, 0, 1, 1},
- {&__pyx_n_s__target_name, __pyx_k__target_name, sizeof(__pyx_k__target_name), 0, 0, 1, 1},
- {&__pyx_n_s__tell, __pyx_k__tell, sizeof(__pyx_k__tell), 0, 0, 1, 1},
{&__pyx_n_s__tempfile, __pyx_k__tempfile, sizeof(__pyx_k__tempfile), 0, 0, 1, 1},
{&__pyx_n_s__template, __pyx_k__template, sizeof(__pyx_k__template), 0, 0, 1, 1},
{&__pyx_n_s__text, __pyx_k__text, sizeof(__pyx_k__text), 0, 0, 1, 1},
- {&__pyx_n_s__theta, __pyx_k__theta, sizeof(__pyx_k__theta), 0, 0, 1, 1},
{&__pyx_n_s__tid, __pyx_k__tid, sizeof(__pyx_k__tid), 0, 0, 1, 1},
{&__pyx_n_s__traceback, __pyx_k__traceback, sizeof(__pyx_k__traceback), 0, 0, 1, 1},
+ {&__pyx_n_s__truncate, __pyx_k__truncate, sizeof(__pyx_k__truncate), 0, 0, 1, 1},
{&__pyx_n_s__types, __pyx_k__types, sizeof(__pyx_k__types), 0, 0, 1, 1},
{&__pyx_n_s__until_eof, __pyx_k__until_eof, sizeof(__pyx_k__until_eof), 0, 0, 1, 1},
+ {&__pyx_n_s__version_info, __pyx_k__version_info, sizeof(__pyx_k__version_info), 0, 0, 1, 1},
{&__pyx_n_s__view, __pyx_k__view, sizeof(__pyx_k__view), 0, 0, 1, 1},
{&__pyx_n_s__w, __pyx_k__w, sizeof(__pyx_k__w), 0, 0, 1, 1},
+ {&__pyx_n_s__warn, __pyx_k__warn, sizeof(__pyx_k__warn), 0, 0, 1, 1},
+ {&__pyx_n_s__warnings, __pyx_k__warnings, sizeof(__pyx_k__warnings), 0, 0, 1, 1},
{&__pyx_n_s__wb, __pyx_k__wb, sizeof(__pyx_k__wb), 0, 0, 1, 1},
{&__pyx_n_s__wbu, __pyx_k__wbu, sizeof(__pyx_k__wbu), 0, 0, 1, 1},
{&__pyx_n_s__wh, __pyx_k__wh, sizeof(__pyx_k__wh), 0, 0, 1, 1},
{&__pyx_n_s__where, __pyx_k__where, sizeof(__pyx_k__where), 0, 0, 1, 1},
{&__pyx_n_s__write, __pyx_k__write, sizeof(__pyx_k__write), 0, 0, 1, 1},
- {&__pyx_n_s__x, __pyx_k__x, sizeof(__pyx_k__x), 0, 0, 1, 1},
+ {&__pyx_n_s__zip, __pyx_k__zip, sizeof(__pyx_k__zip), 0, 0, 1, 1},
{0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
- __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_cmp = __Pyx_GetName(__pyx_b, __pyx_n_s__cmp); if (!__pyx_builtin_cmp) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_chr = __Pyx_GetName(__pyx_b, __pyx_n_s__chr); if (!__pyx_builtin_chr) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ord = __Pyx_GetName(__pyx_b, __pyx_n_s__ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_sorted = __Pyx_GetName(__pyx_b, __pyx_n_s__sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_min = __Pyx_GetName(__pyx_b, __pyx_n_s__min); if (!__pyx_builtin_min) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_max = __Pyx_GetName(__pyx_b, __pyx_n_s__max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_chr = __Pyx_GetName(__pyx_b, __pyx_n_s__chr); if (!__pyx_builtin_chr) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_UnicodeDecodeError = __Pyx_GetName(__pyx_b, __pyx_n_s__UnicodeDecodeError); if (!__pyx_builtin_UnicodeDecodeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
}
-static int __Pyx_InitGlobals(void) {
- if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_13 = PyInt_FromLong(13); if (unlikely(!__pyx_int_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_32 = PyInt_FromLong(32); if (unlikely(!__pyx_int_32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_40 = PyInt_FromLong(40); if (unlikely(!__pyx_int_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_60 = PyInt_FromLong(60); if (unlikely(!__pyx_int_60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_64 = PyInt_FromLong(64); if (unlikely(!__pyx_int_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_128 = PyInt_FromLong(128); if (unlikely(!__pyx_int_128)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_255 = PyInt_FromLong(255); if (unlikely(!__pyx_int_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_256 = PyInt_FromLong(256); if (unlikely(!__pyx_int_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_512 = PyInt_FromLong(512); if (unlikely(!__pyx_int_512)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_neg_127 = PyInt_FromLong(-127); if (unlikely(!__pyx_int_neg_127)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_0660 = PyInt_FromLong(0660); if (unlikely(!__pyx_int_0660)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_1024 = PyInt_FromLong(1024); if (unlikely(!__pyx_int_1024)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_65535 = PyInt_FromLong(65535); if (unlikely(!__pyx_int_65535)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_neg_32767 = PyInt_FromLong(-32767); if (unlikely(!__pyx_int_neg_32767)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_536870912 = PyInt_FromLong(536870912); if (unlikely(!__pyx_int_536870912)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_4294967295 = PyInt_FromString((char *)"4294967295", 0, 0); if (unlikely(!__pyx_int_4294967295)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_neg_2147483648 = PyInt_FromLong(-2147483648); if (unlikely(!__pyx_int_neg_2147483648)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- return 0;
- __pyx_L1_error:;
- return -1;
-}
+static int __Pyx_InitCachedConstants(void) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
+
+ /* "csamtools.pyx":64
+ * return s
+ * elif PyUnicode_Check(s):
+ * return s.encode('ascii') # <<<<<<<<<<<<<<
+ * else:
+ * raise TypeError, u"Argument must be string, bytes or unicode."
+ */
+ __pyx_k_tuple_2 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_2);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_2, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
+
+ /* "csamtools.pyx":84
+ * return s
+ * elif PyBytes_Check(s):
+ * return s.decode('ascii') # <<<<<<<<<<<<<<
+ * else:
+ * # assume unicode
+ */
+ __pyx_k_tuple_4 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_4);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
+
+ /* "csamtools.pyx":398
+ * def __len__(self):
+ * if self.fastafile == NULL:
+ * raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * return faidx_fetch_nseq(self.fastafile)
+ */
+ __pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_8);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
+ PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_8));
+
+ /* "csamtools.pyx":431
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self._filename
+ *
+ */
+ __pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_11);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
+
+ /* "csamtools.pyx":456
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * cdef int length
+ */
+ __pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_12);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
+
+ /* "csamtools.pyx":462
+ *
+ * if not region:
+ * if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
+ * if start is None: start = 0
+ * if end is None: end = max_pos -1
+ */
+ __pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_14);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_13));
+ PyTuple_SET_ITEM(__pyx_k_tuple_14, 0, ((PyObject *)__pyx_kp_s_13));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_13));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
+
+ /* "csamtools.pyx":481
+ * region = "%s:%i-%i" % (reference, start+1, end)
+ * if PY_MAJOR_VERSION >= 3:
+ * region = region.encode('ascii') # <<<<<<<<<<<<<<
+ * seq = fai_fetch( self.fastafile,
+ * region,
+ */
+ __pyx_k_tuple_20 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_20);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
+
+ /* "csamtools.pyx":663
+ * if self._filename != NULL: free(self._filename )
+ * filename = _my_encodeFilename(filename)
+ * cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<<
+ * #cdef char* cfilename
+ * #cfilename = filename.encode(_FILENAME_ENCODING)
+ */
+ __pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_25);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_25, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_25));
+
+ /* "csamtools.pyx":790
+ * returns -1 if reference is not known.
+ * '''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * reference = _force_bytes(reference)
+ * return pysam_reference2tid( self.samfile.header, reference )
+ */
+ __pyx_k_tuple_39 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_39);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_39, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));
+
+ /* "csamtools.pyx":797
+ * '''
+ * convert numerical :term:`tid` into :term:`reference` name.'''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ */
+ __pyx_k_tuple_40 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_40);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_40, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
+
+ /* "csamtools.pyx":805
+ * '''
+ * convert numerical :term:`tid` into :term:`reference` name.'''
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not 0 <= tid < self.samfile.header.n_targets:
+ * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ */
+ __pyx_k_tuple_42 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_42);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_42, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
+
+ /* "csamtools.pyx":855
+ * if len(parts) >= 3: rend = int(parts[2])
+ *
+ * if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
+ *
+ * rtid = self.gettid( reference )
+ */
+ __pyx_k_tuple_44 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_44);
+ __Pyx_INCREF(__pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
+ __Pyx_INCREF(__pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_k_tuple_44, 1, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
+ __Pyx_INCREF(__pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_k_tuple_44, 2, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
+ __Pyx_INCREF(__pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_k_tuple_44, 3, __pyx_int_0);
+ __Pyx_GIVEREF(__pyx_int_0);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
+
+ /* "csamtools.pyx":875
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files")
+ */
+ __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_47);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
+
+ /* "csamtools.pyx":877
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
+ * if self.isstream:
+ * raise OSError("seek no available in streams")
+ */
+ __pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_49);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
+ PyTuple_SET_ITEM(__pyx_k_tuple_49, 0, ((PyObject *)__pyx_kp_s_48));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
+
+ /* "csamtools.pyx":879
+ * raise NotImplementedError("seek only available in bam files")
+ * if self.isstream:
+ * raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
+ *
+ * return bam_seek( self.samfile.x.bam, offset, where )
+ */
+ __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_51);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_50));
+ PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_50));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_50));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
+
+ /* "csamtools.pyx":888
+ * '''
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files")
+ */
+ __pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_52);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
+
+ /* "csamtools.pyx":890
+ * raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam:
+ * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
+ *
+ * return bam_tell( self.samfile.x.bam )
+ */
+ __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_53);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
+ PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_48));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
+
+ /* "csamtools.pyx":925
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ */
+ __pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_55);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
+
+ /* "csamtools.pyx":934
+ * if self.isbam:
+ * if not until_eof and not self._hasIndex() and not self.isremote:
+ * raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
+ *
+ * if callback:
+ */
+ __pyx_k_tuple_57 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_57);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
+ PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, ((PyObject *)__pyx_kp_s_56));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
+
+ /* "csamtools.pyx":937
+ *
+ * if callback:
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * return bam_fetch(self.samfile.x.bam,
+ */
+ __pyx_k_tuple_59 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_59);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
+ PyTuple_SET_ITEM(__pyx_k_tuple_59, 0, ((PyObject *)__pyx_kp_s_58));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));
+
+ /* "csamtools.pyx":938
+ * if callback:
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
+ * return bam_fetch(self.samfile.x.bam,
+ * self.index,
+ */
+ __pyx_k_tuple_61 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_61);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
+ PyTuple_SET_ITEM(__pyx_k_tuple_61, 0, ((PyObject *)__pyx_kp_s_60));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
+
+ /* "csamtools.pyx":957
+ * else:
+ * if has_coord:
+ * raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
+ *
+ * if callback:
+ */
+ __pyx_k_tuple_63 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_63);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_62));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_kp_s_62));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_62));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
+
+ /* "csamtools.pyx":960
+ *
+ * if callback:
+ * raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
+ *
+ * if self.samfile.header == NULL:
+ */
+ __pyx_k_tuple_65 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_65);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_64));
+ PyTuple_SET_ITEM(__pyx_k_tuple_65, 0, ((PyObject *)__pyx_kp_s_64));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_64));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65));
+
+ /* "csamtools.pyx":963
+ *
+ * if self.samfile.header == NULL:
+ * raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
+ *
+ * # check if targets are defined
+ */
+ __pyx_k_tuple_67 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_67);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
+ PyTuple_SET_ITEM(__pyx_k_tuple_67, 0, ((PyObject *)__pyx_kp_s_66));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67));
+
+ /* "csamtools.pyx":968
+ * # give warning, sam_read1 segfaults
+ * if self.samfile.header.n_targets == 0:
+ * warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<<
+ *
+ * return IteratorRowAll( self, reopen=reopen )
+ */
+ __pyx_k_tuple_68 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_68);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
+ PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_kp_s_66));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));
+
+ /* "csamtools.pyx":1009
+ *
+ * if mate_data.mate == NULL:
+ * raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
+ *
+ * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
+ */
+ __pyx_k_tuple_72 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_72);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_71));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_kp_s_71));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_71));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
+
+ /* "csamtools.pyx":1034
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ */
+ __pyx_k_tuple_74 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_74);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74));
+
+ /* "csamtools.pyx":1043
+ * if self.isbam:
+ * if not until_eof and not self._hasIndex() and not self.isremote:
+ * raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
+ *
+ * if not region:
+ */
+ __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_75);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
+ PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_kp_s_56));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
+
+ /* "csamtools.pyx":1046
+ *
+ * if not region:
+ * raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" )
+ * bam_fetch(self.samfile.x.bam,
+ */
+ __pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_77);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
+ PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_kp_s_76));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
+
+ /* "csamtools.pyx":1047
+ * if not region:
+ * raise ValueError( "counting functionality requires a region/reference" )
+ * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
+ * bam_fetch(self.samfile.x.bam,
+ * self.index,
+ */
+ __pyx_k_tuple_78 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_78);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
+ PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_kp_s_60));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
+
+ /* "csamtools.pyx":1057
+ * return counter
+ * else:
+ * raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
+ *
+ * def pileup( self,
+ */
+ __pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_80);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_79));
+ PyTuple_SET_ITEM(__pyx_k_tuple_80, 0, ((PyObject *)__pyx_kp_s_79));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_79));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
+
+ /* "csamtools.pyx":1116
+ *
+ * if not self._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
+ */
+ __pyx_k_tuple_81 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_81);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_81, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_81));
+
+ /* "csamtools.pyx":1121
+ *
+ * if self.isbam:
+ * if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
+ *
+ * if callback:
+ */
+ __pyx_k_tuple_83 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_83);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_82));
+ PyTuple_SET_ITEM(__pyx_k_tuple_83, 0, ((PyObject *)__pyx_kp_s_82));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_82));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83));
+
+ /* "csamtools.pyx":1124
+ *
+ * if callback:
+ * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
+ *
+ * buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback )
+ */
+ __pyx_k_tuple_84 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_84);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
+ PyTuple_SET_ITEM(__pyx_k_tuple_84, 0, ((PyObject *)__pyx_kp_s_58));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_84));
+
+ /* "csamtools.pyx":1145
+ *
+ * else:
+ * raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
+ *
+ * def close( self ):
+ */
+ __pyx_k_tuple_86 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_86);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_85));
+ PyTuple_SET_ITEM(__pyx_k_tuple_86, 0, ((PyObject *)__pyx_kp_s_85));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
+
+ /* "csamtools.pyx":1189
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self._filename
+ *
+ */
+ __pyx_k_tuple_87 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_87);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_87, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
+
+ /* "csamtools.pyx":1195
+ * '''number of :term:`reference` sequences in the file.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self.samfile.header.n_targets
+ *
+ */
+ __pyx_k_tuple_88 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_88);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_88, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_88));
+
+ /* "csamtools.pyx":1201
+ * """tuple with the names of :term:`reference` sequences."""
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ */
+ __pyx_k_tuple_89 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_89);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_89, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89));
+
+ /* "csamtools.pyx":1212
+ * """
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * t = []
+ * for x from 0 <= x < self.samfile.header.n_targets:
+ */
+ __pyx_k_tuple_90 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_90)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_90);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_90, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_90));
+
+ /* "csamtools.pyx":1222
+ * """
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
+ *
+ */
+ __pyx_k_tuple_91 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_91);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_91, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_91));
+
+ /* "csamtools.pyx":1223
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
+ *
+ * cdef int tid
+ */
+ __pyx_k_tuple_93 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_93)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_93);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_92));
+ PyTuple_SET_ITEM(__pyx_k_tuple_93, 0, ((PyObject *)__pyx_kp_s_92));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_93));
+
+ /* "csamtools.pyx":1235
+ * """
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
+ * cdef int tid
+ */
+ __pyx_k_tuple_94 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_94)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_94);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_94, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_94));
+
+ /* "csamtools.pyx":1236
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
+ * cdef int tid
+ * cdef uint32_t total = 0
+ */
+ __pyx_k_tuple_96 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_96);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_95));
+ PyTuple_SET_ITEM(__pyx_k_tuple_96, 0, ((PyObject *)__pyx_kp_s_95));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_95));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
+
+ /* "csamtools.pyx":1248
+ * '''full contents of the :term:`sam file` header as a string.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
+ *
+ */
+ __pyx_k_tuple_97 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_97);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_97, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
+
+ /* "csamtools.pyx":1256
+ * '''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * result = {}
+ */
+ __pyx_k_tuple_98 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_98);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_98, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
+
+ /* "csamtools.pyx":1263
+ * # convert to python string (note: call self.text to create 0-terminated string)
+ * t = self.text
+ * for line in t.split("\n"): # <<<<<<<<<<<<<<
+ * if not line.strip(): continue
+ * assert line.startswith("@"), "header line without '@': '%s'" % line
+ */
+ __pyx_k_tuple_99 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_99);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
+ PyTuple_SET_ITEM(__pyx_k_tuple_99, 0, ((PyObject *)__pyx_kp_s_6));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
+
+ /* "csamtools.pyx":1265
+ * for line in t.split("\n"):
+ * if not line.strip(): continue
+ * assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
+ * fields = line[1:].split("\t")
+ * record = fields[0]
+ */
+ __pyx_k_tuple_101 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_101)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_101);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_100));
+ PyTuple_SET_ITEM(__pyx_k_tuple_101, 0, ((PyObject *)__pyx_kp_s_100));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_100));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_101));
+
+ /* "csamtools.pyx":1266
+ * if not line.strip(): continue
+ * assert line.startswith("@"), "header line without '@': '%s'" % line
+ * fields = line[1:].split("\t") # <<<<<<<<<<<<<<
+ * record = fields[0]
+ * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
+ */
+ __pyx_k_tuple_103 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_103);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
+ PyTuple_SET_ITEM(__pyx_k_tuple_103, 0, ((PyObject *)__pyx_kp_s_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
+
+ /* "csamtools.pyx":1279
+ * x = {}
+ * for field in fields[1:]:
+ * key, value = field.split(":",1) # <<<<<<<<<<<<<<
+ * # uppercase keys must be valid
+ * # lowercase are permitted for user fields
+ */
+ __pyx_k_tuple_106 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_106)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_106);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_105));
+ PyTuple_SET_ITEM(__pyx_k_tuple_106, 0, ((PyObject *)__pyx_kp_s_105));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_105));
+ __Pyx_INCREF(__pyx_int_1);
+ PyTuple_SET_ITEM(__pyx_k_tuple_106, 1, __pyx_int_1);
+ __Pyx_GIVEREF(__pyx_int_1);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_106));
+
+ /* "csamtools.pyx":1377
+ * dest.text = <char*>calloc( len(text), sizeof(char))
+ * dest.l_text = len(text)
+ * cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<<
+ * strncpy( dest.text, btext, dest.l_text )
+ *
+ */
+ __pyx_k_tuple_112 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_112);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_112, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112));
+
+ /* "csamtools.pyx":1397
+ * seqname, seqlen = seqs[x]
+ * dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
+ * bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<<
+ * strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
+ * dest.target_len[x] = seqlen
+ */
+ __pyx_k_tuple_114 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_114)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_114);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_114, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_114));
-#if PY_MAJOR_VERSION < 3
-PyMODINIT_FUNC initcsamtools(void); /*proto*/
-PyMODINIT_FUNC initcsamtools(void)
-#else
-PyMODINIT_FUNC PyInit_csamtools(void); /*proto*/
-PyMODINIT_FUNC PyInit_csamtools(void)
-#endif
-{
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
- #if CYTHON_REFNANNY
- void* __pyx_refnanny = NULL;
- __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
- if (!__Pyx_RefNanny) {
- PyErr_Clear();
- __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
- if (!__Pyx_RefNanny)
- Py_FatalError("failed to import 'refnanny' module");
- }
- __pyx_refnanny = __Pyx_RefNanny->SetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", __LINE__, __FILE__);
- #endif
- __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #ifdef __pyx_binding_PyCFunctionType_USED
- if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- /*--- Library function declarations ---*/
- /*--- Threads initialization code ---*/
- #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
- #ifdef WITH_THREAD /* Python build with threading support? */
- PyEval_InitThreads();
- #endif
- #endif
- /*--- Module creation code ---*/
- #if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
- #else
- __pyx_m = PyModule_Create(&__pyx_moduledef);
- #endif
- if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
- #endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- /*--- Initialize various global constants etc. ---*/
- if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_module_is_main_csamtools) {
- if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- }
- /*--- Builtin init code ---*/
- if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /*--- Global init code ---*/
- /*--- Function export code ---*/
- /*--- Type init code ---*/
- __pyx_ptype_9csamtools_file = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "file", sizeof(PyFileObject), 0); if (unlikely(!__pyx_ptype_9csamtools_file)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_11AlignedRead___str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_11AlignedRead___str__.doc = __pyx_doc_9csamtools_11AlignedRead___str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead___str__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
- __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
- __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
- __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
- __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
- __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile._buildHeader = (void(*)(void))__pyx_f_9csamtools_7Samfile__buildHeader;
- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.getCurrent = (void(*)(void))__pyx_f_9csamtools_7Samfile_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.cnext = (void(*)(void))__pyx_f_9csamtools_7Samfile_cnext;
- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.write = (void(*)(void))__pyx_f_9csamtools_7Samfile_write;
- *(void(**)(void))&__pyx_vtable_9csamtools_Samfile._getrname = (void(*)(void))__pyx_f_9csamtools_7Samfile__getrname;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_7Samfile___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_7Samfile___next__.doc = __pyx_doc_9csamtools_7Samfile___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
- __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_Fastafile._fetch = (void(*)(void))__pyx_f_9csamtools_9Fastafile__fetch;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
- __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.cnext = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
- __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__.doc = __pyx_doc_9csamtools_14IteratorRowAll___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
- __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
- __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.cnext = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- #endif
- __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
- __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
- __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
- __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_cnext;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.getSequence = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setMask = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setMask;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.reset = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_reset;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
- __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
- __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion;
- __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs;
- __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
- __pyx_vtabptr_9csamtools_SNPCallerBase = &__pyx_vtable_9csamtools_SNPCallerBase;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_SNPCallerBase.__dump = (PyObject *(*)(struct __pyx_obj_9csamtools_SNPCallerBase *, glf1_t *, uint32_t, int))__pyx_f_9csamtools_13SNPCallerBase___dump;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_SNPCallerBase.__dump = (void(*)(void))__pyx_f_9csamtools_13SNPCallerBase___dump;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCallerBase.tp_dict, __pyx_vtabptr_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCallerBase", (PyObject *)&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCallerBase = &__pyx_type_9csamtools_SNPCallerBase;
- __pyx_vtabptr_9csamtools_IteratorSNPCalls = &__pyx_vtable_9csamtools_IteratorSNPCalls;
- __pyx_vtable_9csamtools_IteratorSNPCalls.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase;
- __pyx_type_9csamtools_IteratorSNPCalls.tp_base = __pyx_ptype_9csamtools_SNPCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__.doc = __pyx_doc_9csamtools_16IteratorSNPCalls___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorSNPCalls.tp_dict, __pyx_vtabptr_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorSNPCalls", (PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorSNPCalls = &__pyx_type_9csamtools_IteratorSNPCalls;
- __pyx_vtabptr_9csamtools_SNPCaller = &__pyx_vtable_9csamtools_SNPCaller;
- __pyx_vtable_9csamtools_SNPCaller.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase;
- __pyx_type_9csamtools_SNPCaller.tp_base = __pyx_ptype_9csamtools_SNPCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCaller.tp_dict, __pyx_vtabptr_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCaller", (PyObject *)&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCaller = &__pyx_type_9csamtools_SNPCaller;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCall", (PyObject *)&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndelCall = &__pyx_type_9csamtools_IndelCall;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCallerBase", (PyObject *)&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndelCallerBase = &__pyx_type_9csamtools_IndelCallerBase;
- __pyx_type_9csamtools_IndelCaller.tp_base = __pyx_ptype_9csamtools_IndelCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCaller", (PyObject *)&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndelCaller = &__pyx_type_9csamtools_IndelCaller;
- __pyx_type_9csamtools_IteratorIndelCalls.tp_base = __pyx_ptype_9csamtools_IndelCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorIndelCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorIndelCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__.doc = __pyx_doc_9csamtools_18IteratorIndelCalls___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "IteratorIndelCalls", (PyObject *)&__pyx_type_9csamtools_IteratorIndelCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorIndelCalls = &__pyx_type_9csamtools_IteratorIndelCalls;
- if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndexedReads = &__pyx_type_9csamtools_IndexedReads;
- /*--- Type import code ---*/
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /*--- Function import code ---*/
- /*--- Execution code ---*/
+ /* "csamtools.pyx":1412
+ * ###############################################################
+ * def __iter__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * if not self.isbam and self.samfile.header.n_targets == 0:
+ * raise NotImplementedError( "can not iterate over samfile without header")
+ */
+ __pyx_k_tuple_115 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_115)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_115);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_115, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_115));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":4
- * # cython: profile=True
- * # adds doc-strings for sphinx
- * import tempfile # <<<<<<<<<<<<<<
- * import os
- * import sys
+ /* "csamtools.pyx":1414
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam and self.samfile.header.n_targets == 0:
+ * raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<<
+ * return self
+ *
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tempfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_117 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_117);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_116));
+ PyTuple_SET_ITEM(__pyx_k_tuple_117, 0, ((PyObject *)__pyx_kp_s_116));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_116));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":5
- * # adds doc-strings for sphinx
- * import tempfile
- * import os # <<<<<<<<<<<<<<
- * import sys
- * import types
+ /* "csamtools.pyx":1484
+ *
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * if not samfile._hasIndex():
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__os), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__os, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_118 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_118)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_118);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_118, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_118));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":6
- * import tempfile
- * import os
- * import sys # <<<<<<<<<<<<<<
- * import types
- * import itertools
+ /* "csamtools.pyx":1487
+ *
+ * if not samfile._hasIndex():
+ * raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
+ *
+ * # makes sure that samfile stays alive as long as the
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sys, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_120 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_120);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_119));
+ PyTuple_SET_ITEM(__pyx_k_tuple_120, 0, ((PyObject *)__pyx_kp_s_119));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_119));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_120));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":7
- * import os
- * import sys
- * import types # <<<<<<<<<<<<<<
- * import itertools
- * import struct
+ /* "csamtools.pyx":1553
+ *
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * if samfile.isbam: mode = b"rb"
+ */
+ __pyx_k_tuple_121 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_121)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_121);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_121, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_121));
+
+ /* "csamtools.pyx":1604
+ * def __cinit__(self, Samfile samfile):
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ * self.tid = -1
+ */
+ __pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_122);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
+ PyTuple_SET_ITEM(__pyx_k_tuple_122, 0, ((PyObject *)__pyx_kp_s_60));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
+
+ /* "csamtools.pyx":1650
+ *
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+ __pyx_k_tuple_123 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_123)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_123);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_123, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_123));
+
+ /* "csamtools.pyx":1653
+ *
+ * if not samfile._isOpen():
+ * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ *
+ * assert samfile.isbam, "can only use this iterator on bam files"
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__types), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__types, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_124 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_124);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
+ PyTuple_SET_ITEM(__pyx_k_tuple_124, 0, ((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":8
- * import sys
- * import types
- * import itertools # <<<<<<<<<<<<<<
- * import struct
- * import ctypes
+ /* "csamtools.pyx":1954
+ * self.cnext()
+ * if self.n_plp < 0:
+ * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
+ *
+ * if self.plp == NULL:
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__itertools), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__itertools, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_130 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_130)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_130);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
+ PyTuple_SET_ITEM(__pyx_k_tuple_130, 0, ((PyObject *)__pyx_kp_s_129));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_130));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":9
- * import types
- * import itertools
- * import struct # <<<<<<<<<<<<<<
- * import ctypes
- * import collections
+ /* "csamtools.pyx":1990
+ *
+ * if self.n_plp < 0:
+ * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
+ *
+ * # return result, if within same reference
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__struct), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__struct, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_131 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_131);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
+ PyTuple_SET_ITEM(__pyx_k_tuple_131, 0, ((PyObject *)__pyx_kp_s_129));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":10
- * import itertools
- * import struct
- * import ctypes # <<<<<<<<<<<<<<
- * import collections
- * import re
+ /* "csamtools.pyx":2153
+ * qual = self.qual
+ * else:
+ * seq = self.seq.decode('ascii') # <<<<<<<<<<<<<<
+ * qual = self.qual.decode('ascii')
+ * return "\t".join(map(str, (self.qname,
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__ctypes), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__ctypes, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_133 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_133);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_133, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_133));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":11
- * import struct
- * import ctypes
- * import collections # <<<<<<<<<<<<<<
- * import re
- * import platform
+ /* "csamtools.pyx":2154
+ * else:
+ * seq = self.seq.decode('ascii')
+ * qual = self.qual.decode('ascii') # <<<<<<<<<<<<<<
+ * return "\t".join(map(str, (self.qname,
+ * self.flag,
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__collections), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__collections, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_134 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_134)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_134);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_134, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_134));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":12
- * import ctypes
- * import collections
- * import re # <<<<<<<<<<<<<<
- * import platform
- * from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
+ /* "csamtools.pyx":2563
+ * for pytag, value in tags:
+ * if not type(pytag) is bytes:
+ * pytag = pytag.encode('ascii') # <<<<<<<<<<<<<<
+ * t = type(value)
+ *
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__re), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__re, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_139 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_139);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_139, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_139));
+
+ /* "csamtools.pyx":2591
+ * datafmt = "2sccI%i%s" % (len(value), datafmt)
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'), # <<<<<<<<<<<<<<
+ * datatype.encode('ascii'),
+ * len(value)] + list(value) )
+ */
+ __pyx_k_tuple_142 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_142)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_142);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_142, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_142));
+
+ /* "csamtools.pyx":2592
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'),
+ * datatype.encode('ascii'), # <<<<<<<<<<<<<<
+ * len(value)] + list(value) )
+ * fmts.append( datafmt )
+ */
+ __pyx_k_tuple_143 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_143)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_143);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_143, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_143));
+
+ /* "csamtools.pyx":2615
+ * # Note: hex strings (H) are not supported yet
+ * if t is not bytes:
+ * value = value.encode('ascii') # <<<<<<<<<<<<<<
+ * if len(value) == 1:
+ * fmt, pytype = "2scc", 'A'
+ */
+ __pyx_k_tuple_144 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_144)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_144);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_144, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_144));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":13
- * import collections
- * import re
- * import platform # <<<<<<<<<<<<<<
- * from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
- * from cpython cimport PyErr_SetString
+ /* "csamtools.pyx":2622
+ *
+ * args.extend( [pytag[:2],
+ * pytype.encode('ascii'), # <<<<<<<<<<<<<<
+ * value ] )
+ *
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__platform), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__platform, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_146 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_146)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_146);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ PyTuple_SET_ITEM(__pyx_k_tuple_146, 0, ((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_146));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":63
- * #####################################################################
- * # hard-coded constants
- * cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN" # <<<<<<<<<<<<<<
- * cdef int max_pos = 2 << 29
+ /* "csamtools.pyx":3020
+ * '''
+ * def __init__(self):
+ * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
*
+ * def __str__(self):
*/
- __pyx_v_9csamtools_bam_nt16_rev_table = __pyx_k_172;
+ __pyx_k_tuple_172 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_172)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_172);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
+ PyTuple_SET_ITEM(__pyx_k_tuple_172, 0, ((PyObject *)__pyx_kp_s_171));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_172));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":64
- * # hard-coded constants
- * cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN"
- * cdef int max_pos = 2 << 29 # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3046
*
- * # redirect stderr to 0
+ * if self.plp[0] == NULL:
+ * raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<<
+ *
+ * # warning: there could be problems if self.n and self.buf are
*/
- __pyx_v_9csamtools_max_pos = 1073741824;
+ __pyx_k_tuple_174 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_174);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_173));
+ PyTuple_SET_ITEM(__pyx_k_tuple_174, 0, ((PyObject *)__pyx_kp_s_173));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_173));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_174));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":67
+ /* "csamtools.pyx":3059
*
- * # redirect stderr to 0
- * _logfile = open(os.path.devnull, "w") # <<<<<<<<<<<<<<
- * pysam_set_stderr( PyFile_AsFile( _logfile ) )
+ * def __init__(self):
+ * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
*
+ * def __str__(self):
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__devnull); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__w));
- PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__w));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__w));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_open, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s___logfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_175 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_175);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
+ PyTuple_SET_ITEM(__pyx_k_tuple_175, 0, ((PyObject *)__pyx_kp_s_171));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_175));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":68
- * # redirect stderr to 0
- * _logfile = open(os.path.devnull, "w")
- * pysam_set_stderr( PyFile_AsFile( _logfile ) ) # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":3172
+ * # recover. Thus redirect output to file with -o option.
+ * if method == "view":
+ * if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
+ * args = ( "-o", stdout_f ) + args
*
- * #####################################################################
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s___logfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- pysam_set_stderr(PyFile_AsFile(__pyx_t_1));
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_k_tuple_180 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_180);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_179));
+ PyTuple_SET_ITEM(__pyx_k_tuple_180, 0, ((PyObject *)__pyx_kp_s_179));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_179));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_180));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":117
- * (<object>f)(a)
+ /* "csamtools.pyx":3197
+ * stdout_save.restore()
+ * try:
+ * with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError:
+ */
+ __pyx_k_tuple_181 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_181);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_181, 0, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_181, 1, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_181, 2, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181));
+
+ /* "csamtools.pyx":3200
+ * out_stdout = inf.readlines()
+ * except UnicodeDecodeError:
+ * with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
+ * # read binary output
+ * out_stdout = inf.read()
+ */
+ __pyx_k_tuple_182 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_182);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_182, 0, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_182, 1, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_182, 2, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_182));
+
+ /* "csamtools.pyx":3210
+ * pysam_unset_stderr()
+ * try:
+ * with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError:
+ */
+ __pyx_k_tuple_183 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_183);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_183, 0, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_183, 1, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_183, 2, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_183));
+
+ /* "csamtools.pyx":3213
+ * out_stderr = inf.readlines()
+ * except UnicodeDecodeError:
+ * with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
+ * # read binary output
+ * out_stderr = inf.read()
+ */
+ __pyx_k_tuple_184 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_184);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_184, 0, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_184, 1, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_INCREF(Py_None);
+ PyTuple_SET_ITEM(__pyx_k_tuple_184, 2, Py_None);
+ __Pyx_GIVEREF(Py_None);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_184));
+
+ /* "csamtools.pyx":143
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) # <<<<<<<<<<<<<<
*
- * class PileupColumn(object): # <<<<<<<<<<<<<<
- * '''A pileup column. A pileup column contains
- * all the reads that map to a certain target base.
+ * #####################################################################
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_builtin_object);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_object);
- __Pyx_GIVEREF(__pyx_builtin_object);
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_173)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_CreateClass(__pyx_t_2, ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, "csamtools"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_k_tuple_252 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_252);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_251));
+ PyTuple_SET_ITEM(__pyx_k_tuple_252, 0, ((PyObject *)__pyx_kp_s_251));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_251));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_252));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":130
+ /* "csamtools.pyx":260
* list of reads (:class:`pysam.PileupRead`) aligned to this column
* '''
* def __str__(self): # <<<<<<<<<<<<<<
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_12PileupColumn___str__, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s____str__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PileupColumn, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":174
- * return 0
- *
- * class StderrStore(): # <<<<<<<<<<<<<<
- * '''
- * stderr is captured.
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_174)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, "csamtools"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_k_tuple_254 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_254);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_254, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_254));
+ __pyx_k_codeobj_255 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_254, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____str__, 260, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":178
+ /* "csamtools.pyx":308
* stderr is captured.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
* return
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
- __pyx_t_4 = PyCFunction_New(&__pyx_mdef_9csamtools_11StderrStore___init__, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyMethod_New(__pyx_t_4, 0, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s____init__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_k_tuple_258 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_258);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
+ __pyx_k_codeobj_259 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_258, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 308, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":184
+ /* "csamtools.pyx":314
* self.stderr_save.setfd( self.stderr_h )
*
* def readAndRelease( self ): # <<<<<<<<<<<<<<
* return []
* self.stderr_save.restore()
*/
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_11StderrStore_readAndRelease, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_k_tuple_260 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_260);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_260));
+ __pyx_k_codeobj_261 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_260, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__readAndRelease, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_261)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":193
+ /* "csamtools.pyx":323
* return lines
*
* def release(self): # <<<<<<<<<<<<<<
* return
* self.stderr_save.restore()
*/
- __pyx_t_4 = PyCFunction_New(&__pyx_mdef_9csamtools_11StderrStore_release, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyMethod_New(__pyx_t_4, 0, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s__release, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_k_tuple_262 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_262)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_262);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_262, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_262));
+ __pyx_k_codeobj_263 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_262, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__release, 323, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_263)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":199
+ /* "csamtools.pyx":329
* os.remove( self.stderr_f )
*
* def __del__(self): # <<<<<<<<<<<<<<
* self.release()
*
*/
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_11StderrStore___del__, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s____del__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":202
- * self.release()
- *
- * class StderrStoreWindows(): # <<<<<<<<<<<<<<
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_175)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, "csamtools"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_k_tuple_264 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_264)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_264);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_264, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_264));
+ __pyx_k_codeobj_265 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_264, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____del__, 329, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_265)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":204
+ /* "csamtools.pyx":334
* class StderrStoreWindows():
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass # <<<<<<<<<<<<<<
* def readAndRelease(self): return []
- * def release(self): pass
- */
- __pyx_t_4 = PyCFunction_New(&__pyx_mdef_9csamtools_18StderrStoreWindows___init__, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyMethod_New(__pyx_t_4, 0, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s____init__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":205
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass
- * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
- * def release(self): pass
- *
- */
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_18StderrStoreWindows_readAndRelease, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":206
- * def __init__(self): pass
- * def readAndRelease(self): return []
- * def release(self): pass # <<<<<<<<<<<<<<
- *
- * if platform.system()=='Windows':
- */
- __pyx_t_4 = PyCFunction_New(&__pyx_mdef_9csamtools_18StderrStoreWindows_release, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyMethod_New(__pyx_t_4, 0, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_t_3, __pyx_n_s__release, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStoreWindows, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":208
- * def release(self): pass
- *
- * if platform.system()=='Windows': # <<<<<<<<<<<<<<
- * del StderrStore
- * StderrStore = StderrStoreWindows
- */
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__platform); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__system); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Windows), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_5) {
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":209
- *
- * if platform.system()=='Windows':
- * del StderrStore # <<<<<<<<<<<<<<
- * StderrStore = StderrStoreWindows
- *
- */
- if (__Pyx_DelAttrString(__pyx_m, "StderrStore") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":210
- * if platform.system()=='Windows':
- * del StderrStore
- * StderrStore = StderrStoreWindows # <<<<<<<<<<<<<<
- *
- *
- */
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStoreWindows); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L2;
- }
- __pyx_L2:;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":217
- * ######################################################################
- * # valid types for sam headers
- * VALID_HEADER_TYPES = { "HD" : dict, # <<<<<<<<<<<<<<
- * "SQ" : list,
- * "RG" : list,
- */
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)&PyDict_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":218
- * # valid types for sam headers
- * VALID_HEADER_TYPES = { "HD" : dict,
- * "SQ" : list, # <<<<<<<<<<<<<<
- * "RG" : list,
- * "PG" : list,
- */
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)&PyList_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":219
- * VALID_HEADER_TYPES = { "HD" : dict,
- * "SQ" : list,
- * "RG" : list, # <<<<<<<<<<<<<<
- * "PG" : list,
- * "CO" : list }
- */
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)&PyList_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":220
- * "SQ" : list,
- * "RG" : list,
- * "PG" : list, # <<<<<<<<<<<<<<
- * "CO" : list }
+ * def release(self): pass
+ */
+ __pyx_k_tuple_267 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_267)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_267);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_267, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_267));
+ __pyx_k_codeobj_268 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_267, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 334, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_268)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":335
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass
+ * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
+ * def release(self): pass
*
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)&PyList_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_269 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_269)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_269);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_269, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_269));
+ __pyx_k_codeobj_270 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_269, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__readAndRelease, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_270)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":221
- * "RG" : list,
- * "PG" : list,
- * "CO" : list } # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":336
+ * def __init__(self): pass
+ * def readAndRelease(self): return []
+ * def release(self): pass # <<<<<<<<<<<<<<
*
- * # order of records within sam headers
+ * if platform.system()=='Windows':
*/
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)&PyList_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_k_tuple_271 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_271)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_271);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_271, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_271));
+ __pyx_k_codeobj_272 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_271, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__release, 336, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_272)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":224
+ /* "csamtools.pyx":354
*
* # order of records within sam headers
* VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<<
*
* # type conversions within sam header records
*/
- __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_k_tuple_274 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_274)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_274);
__Pyx_INCREF(((PyObject *)__pyx_n_s__HD));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_n_s__HD));
+ PyTuple_SET_ITEM(__pyx_k_tuple_274, 0, ((PyObject *)__pyx_n_s__HD));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__HD));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SQ));
- PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__SQ));
+ PyTuple_SET_ITEM(__pyx_k_tuple_274, 1, ((PyObject *)__pyx_n_s__SQ));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SQ));
__Pyx_INCREF(((PyObject *)__pyx_n_s__RG));
- PyTuple_SET_ITEM(__pyx_t_3, 2, ((PyObject *)__pyx_n_s__RG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_274, 2, ((PyObject *)__pyx_n_s__RG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__RG));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
- PyTuple_SET_ITEM(__pyx_t_3, 3, ((PyObject *)__pyx_n_s__PG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_274, 3, ((PyObject *)__pyx_n_s__PG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CO));
- PyTuple_SET_ITEM(__pyx_t_3, 4, ((PyObject *)__pyx_n_s__CO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_274, 4, ((PyObject *)__pyx_n_s__CO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CO));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":227
- *
- * # type conversions within sam header records
- * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, # <<<<<<<<<<<<<<
- * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
- * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, },
- */
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":228
- * # type conversions within sam header records
- * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
- * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, # <<<<<<<<<<<<<<
- * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, },
- * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)&PyInt_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":229
- * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
- * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
- * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, }, # <<<<<<<<<<<<<<
- * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
- *
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":230
- * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
- * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, },
- * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } # <<<<<<<<<<<<<<
- *
- * # output order of fields within records
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)&PyString_Type))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_274));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":233
+ /* "csamtools.pyx":364
*
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
*/
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_tuple_275 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_275)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_275);
__Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__VN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_275, 0, ((PyObject *)__pyx_n_s__VN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SO));
- PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__SO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_275, 1, ((PyObject *)__pyx_n_s__SO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SO));
__Pyx_INCREF(((PyObject *)__pyx_n_s__GO));
- PyTuple_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__GO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_275, 2, ((PyObject *)__pyx_n_s__GO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__GO));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__HD), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_275));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":234
+ /* "csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
* "PG" : ( "PN", "ID", "VN", "CL" ), }
*/
- __pyx_t_1 = PyTuple_New(6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_tuple_276 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_276)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_276);
__Pyx_INCREF(((PyObject *)__pyx_n_s__SN));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__SN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_276, 0, ((PyObject *)__pyx_n_s__SN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__LN));
- PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__LN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_276, 1, ((PyObject *)__pyx_n_s__LN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__LN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__AS));
- PyTuple_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__AS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_276, 2, ((PyObject *)__pyx_n_s__AS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__AS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__M5));
- PyTuple_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__M5));
+ PyTuple_SET_ITEM(__pyx_k_tuple_276, 3, ((PyObject *)__pyx_n_s__M5));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__M5));
__Pyx_INCREF(((PyObject *)__pyx_n_s__UR));
- PyTuple_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__UR));
+ PyTuple_SET_ITEM(__pyx_k_tuple_276, 4, ((PyObject *)__pyx_n_s__UR));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__UR));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SP));
- PyTuple_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__SP));
+ PyTuple_SET_ITEM(__pyx_k_tuple_276, 5, ((PyObject *)__pyx_n_s__SP));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SP));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__SQ), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_276));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":235
+ /* "csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" ), # <<<<<<<<<<<<<<
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), # <<<<<<<<<<<<<<
* "PG" : ( "PN", "ID", "VN", "CL" ), }
*
*/
- __pyx_t_1 = PyTuple_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_tuple_277 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_277)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_277);
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__ID));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 0, ((PyObject *)__pyx_n_s__ID));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SM));
- PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__SM));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 1, ((PyObject *)__pyx_n_s__SM));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SM));
__Pyx_INCREF(((PyObject *)__pyx_n_s__LB));
- PyTuple_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__LB));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 2, ((PyObject *)__pyx_n_s__LB));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__LB));
__Pyx_INCREF(((PyObject *)__pyx_n_s__DS));
- PyTuple_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__DS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 3, ((PyObject *)__pyx_n_s__DS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__DS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PU));
- PyTuple_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__PU));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 4, ((PyObject *)__pyx_n_s__PU));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PU));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PI));
- PyTuple_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__PI));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 5, ((PyObject *)__pyx_n_s__PI));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PI));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CN));
- PyTuple_SET_ITEM(__pyx_t_1, 6, ((PyObject *)__pyx_n_s__CN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 6, ((PyObject *)__pyx_n_s__CN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__DT));
- PyTuple_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__DT));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 7, ((PyObject *)__pyx_n_s__DT));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__DT));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PL));
- PyTuple_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__PL));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 8, ((PyObject *)__pyx_n_s__PL));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PL));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__RG), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":236
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__FO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 9, ((PyObject *)__pyx_n_s__FO));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__FO));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__KS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_277, 10, ((PyObject *)__pyx_n_s__KS));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__KS));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_277));
+
+ /* "csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
* "PG" : ( "PN", "ID", "VN", "CL" ), } # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_tuple_278 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_278)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_278);
__Pyx_INCREF(((PyObject *)__pyx_n_s__PN));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__PN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_278, 0, ((PyObject *)__pyx_n_s__PN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__ID));
+ PyTuple_SET_ITEM(__pyx_k_tuple_278, 1, ((PyObject *)__pyx_n_s__ID));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
__Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__VN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_278, 2, ((PyObject *)__pyx_n_s__VN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CL));
- PyTuple_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__CL));
+ PyTuple_SET_ITEM(__pyx_k_tuple_278, 3, ((PyObject *)__pyx_n_s__CL));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CL));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__PG), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":719
- * region = None,
- * callback = None,
- * until_eof = False ): # <<<<<<<<<<<<<<
- * '''
- * fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by
- */
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_k_29 = __pyx_t_3;
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":830
- * end = None,
- * region = None,
- * until_eof = False ): # <<<<<<<<<<<<<<
- * '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
- *
- */
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_k_39 = __pyx_t_3;
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1718
- * int tid = 0,
- * int start = 0,
- * int end = max_pos, # <<<<<<<<<<<<<<
- * **kwargs ):
- *
- */
- __pyx_k_58 = __pyx_v_9csamtools_max_pos;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2699
- * return self._level
- *
- * class Outs: # <<<<<<<<<<<<<<
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1):
- */
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- if (PyDict_SetItemString(((PyObject *)__pyx_t_3), "__doc__", ((PyObject *)__pyx_kp_s_176)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_3), __pyx_n_s__Outs, "csamtools"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_278));
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2701
+ /* "csamtools.pyx":3092
* class Outs:
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1): # <<<<<<<<<<<<<<
* self.streams = []
* self.id = id
*/
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_4Outs___init__, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2705
+ __pyx_k_tuple_279 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_279)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_279);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_279, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__id));
+ PyTuple_SET_ITEM(__pyx_k_tuple_279, 1, ((PyObject *)__pyx_n_s__id));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_279));
+ __pyx_k_codeobj_280 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_279, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 3092, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_280)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_281 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_281)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_281);
+ __Pyx_INCREF(((PyObject *)__pyx_int_1));
+ PyTuple_SET_ITEM(__pyx_k_tuple_281, 0, ((PyObject *)__pyx_int_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_int_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_281));
+
+ /* "csamtools.pyx":3096
* self.id = id
*
* def setdevice(self, filename): # <<<<<<<<<<<<<<
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY)
*/
- __pyx_t_4 = PyCFunction_New(&__pyx_mdef_9csamtools_4Outs_setdevice, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyMethod_New(__pyx_t_4, 0, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_t_1, __pyx_n_s__setdevice, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2710
+ __pyx_k_tuple_282 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_282)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_282);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_282, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
+ PyTuple_SET_ITEM(__pyx_k_tuple_282, 1, ((PyObject *)__pyx_n_s__filename));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
+ PyTuple_SET_ITEM(__pyx_k_tuple_282, 2, ((PyObject *)__pyx_n_s__fd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_282));
+ __pyx_k_codeobj_283 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_282, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setdevice, 3096, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_283)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3101
* self.setfd(fd)
*
* def setfile(self, filename): # <<<<<<<<<<<<<<
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
*/
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_4Outs_setfile, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_1, __pyx_n_s__setfile, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2715
+ __pyx_k_tuple_284 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_284)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_284);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_284, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
+ PyTuple_SET_ITEM(__pyx_k_tuple_284, 1, ((PyObject *)__pyx_n_s__filename));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
+ PyTuple_SET_ITEM(__pyx_k_tuple_284, 2, ((PyObject *)__pyx_n_s__fd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_284));
+ __pyx_k_codeobj_285 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_284, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setfile, 3101, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_285)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3106
* self.setfd(fd)
*
* def setfd(self, fd): # <<<<<<<<<<<<<<
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd)
*/
- __pyx_t_4 = PyCFunction_New(&__pyx_mdef_9csamtools_4Outs_setfd, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyMethod_New(__pyx_t_4, 0, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_t_1, __pyx_n_s__setfd, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2723
+ __pyx_k_tuple_286 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_286)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_286);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_286, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
+ PyTuple_SET_ITEM(__pyx_k_tuple_286, 1, ((PyObject *)__pyx_n_s__fd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ofd));
+ PyTuple_SET_ITEM(__pyx_k_tuple_286, 2, ((PyObject *)__pyx_n_s__ofd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ofd));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_286));
+ __pyx_k_codeobj_287 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_286, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setfd, 3106, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_287)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3114
* os.close(fd) # Close other unit (look out, caller.)
*
* def restore(self): # <<<<<<<<<<<<<<
* '''restore previous output stream'''
* if self.streams:
*/
- __pyx_t_2 = PyCFunction_New(&__pyx_mdef_9csamtools_4Outs_restore, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyMethod_New(__pyx_t_2, 0, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_t_1, __pyx_n_s__restore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_k_tuple_288 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_288)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_288);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_288, 0, ((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_288));
+ __pyx_k_codeobj_289 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_288, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__restore, 3114, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_289)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2736
- * def _samtools_dispatch( method,
+ /* "csamtools.pyx":3125
+ * del self.streams[-1]
+ *
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
* args = (),
- * catch_stdout = True, # <<<<<<<<<<<<<<
- * catch_stderr = False,
- * ):
- */
- __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_k_98 = __pyx_t_3;
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
+ * catch_stdout = True ):
+ */
+ __pyx_k_tuple_291 = PyTuple_New(16); if (unlikely(!__pyx_k_tuple_291)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_291);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__method));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 0, ((PyObject *)__pyx_n_s__method));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__method));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__args));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 1, ((PyObject *)__pyx_n_s__args));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__args));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__catch_stdout));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 2, ((PyObject *)__pyx_n_s__catch_stdout));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__catch_stdout));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__stderr_h));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 3, ((PyObject *)__pyx_n_s__stderr_h));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stderr_h));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__stderr_f));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 4, ((PyObject *)__pyx_n_s__stderr_f));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stderr_f));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_h));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 5, ((PyObject *)__pyx_n_s__stdout_h));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_h));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_f));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 6, ((PyObject *)__pyx_n_s__stdout_f));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_f));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_save));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 7, ((PyObject *)__pyx_n_s__stdout_save));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_save));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__cargs));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 8, ((PyObject *)__pyx_n_s__cargs));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cargs));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 9, ((PyObject *)__pyx_n_s__i));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__n));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 10, ((PyObject *)__pyx_n_s__n));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__retval));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 11, ((PyObject *)__pyx_n_s__retval));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__retval));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__inf));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 12, ((PyObject *)__pyx_n_s__inf));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__inf));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__out_stdout));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 13, ((PyObject *)__pyx_n_s__out_stdout));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__out_stdout));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__out_stderr));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 14, ((PyObject *)__pyx_n_s__out_stderr));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__out_stderr));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__a));
+ PyTuple_SET_ITEM(__pyx_k_tuple_291, 15, ((PyObject *)__pyx_n_s__a));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_291));
+ __pyx_k_codeobj_292 = (PyObject*)__Pyx_PyCode_New(3, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_291, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s___samtools_dispatch, 3125, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannyFinishContext();
+ return 0;
+ __pyx_L1_error:;
+ __Pyx_RefNannyFinishContext();
+ return -1;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2737
- * args = (),
- * catch_stdout = True,
- * catch_stderr = False, # <<<<<<<<<<<<<<
- * ):
- * '''call ``method`` in samtools providing arguments in args.
- */
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_k_99 = __pyx_t_3;
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
+static int __Pyx_InitGlobals(void) {
+ if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_32 = PyInt_FromLong(32); if (unlikely(!__pyx_int_32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_64 = PyInt_FromLong(64); if (unlikely(!__pyx_int_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_128 = PyInt_FromLong(128); if (unlikely(!__pyx_int_128)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_255 = PyInt_FromLong(255); if (unlikely(!__pyx_int_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_256 = PyInt_FromLong(256); if (unlikely(!__pyx_int_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_512 = PyInt_FromLong(512); if (unlikely(!__pyx_int_512)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_neg_127 = PyInt_FromLong(-127); if (unlikely(!__pyx_int_neg_127)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_0660 = PyInt_FromLong(0660); if (unlikely(!__pyx_int_0660)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1024 = PyInt_FromLong(1024); if (unlikely(!__pyx_int_1024)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_8000 = PyInt_FromLong(8000); if (unlikely(!__pyx_int_8000)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_65535 = PyInt_FromLong(65535); if (unlikely(!__pyx_int_65535)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_neg_32767 = PyInt_FromLong(-32767); if (unlikely(!__pyx_int_neg_32767)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_536870912 = PyInt_FromLong(536870912); if (unlikely(!__pyx_int_536870912)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_4294967295 = PyInt_FromString((char *)"4294967295", 0, 0); if (unlikely(!__pyx_int_4294967295)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_neg_2147483648 = PyInt_FromLong(-2147483648); if (unlikely(!__pyx_int_neg_2147483648)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3436
- * if self.owns_samfile: samclose( self.fp )
- *
- * __all__ = ["Samfile", # <<<<<<<<<<<<<<
- * "Fastafile",
- * "IteratorRow",
- */
- __pyx_t_3 = PyList_New(13); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile));
- PyList_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_n_s__Samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Samfile));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__Fastafile));
- PyList_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__Fastafile));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Fastafile));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorRow));
- PyList_SET_ITEM(__pyx_t_3, 2, ((PyObject *)__pyx_n_s__IteratorRow));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorRow));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorColumn));
- PyList_SET_ITEM(__pyx_t_3, 3, ((PyObject *)__pyx_n_s__IteratorColumn));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorColumn));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__AlignedRead));
- PyList_SET_ITEM(__pyx_t_3, 4, ((PyObject *)__pyx_n_s__AlignedRead));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__AlignedRead));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PileupColumn));
- PyList_SET_ITEM(__pyx_t_3, 5, ((PyObject *)__pyx_n_s__PileupColumn));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupColumn));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PileupProxy));
- PyList_SET_ITEM(__pyx_t_3, 6, ((PyObject *)__pyx_n_s__PileupProxy));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupProxy));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PileupRead));
- PyList_SET_ITEM(__pyx_t_3, 7, ((PyObject *)__pyx_n_s__PileupRead));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupRead));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorSNPCalls));
- PyList_SET_ITEM(__pyx_t_3, 8, ((PyObject *)__pyx_n_s__IteratorSNPCalls));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorSNPCalls));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__SNPCaller));
- PyList_SET_ITEM(__pyx_t_3, 9, ((PyObject *)__pyx_n_s__SNPCaller));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__SNPCaller));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__IndelCaller));
- PyList_SET_ITEM(__pyx_t_3, 10, ((PyObject *)__pyx_n_s__IndelCaller));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndelCaller));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorIndelCalls));
- PyList_SET_ITEM(__pyx_t_3, 11, ((PyObject *)__pyx_n_s__IteratorIndelCalls));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorIndelCalls));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__IndexedReads));
- PyList_SET_ITEM(__pyx_t_3, 12, ((PyObject *)__pyx_n_s__IndexedReads));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndexedReads));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+#if PY_MAJOR_VERSION < 3
+PyMODINIT_FUNC initcsamtools(void); /*proto*/
+PyMODINIT_FUNC initcsamtools(void)
+#else
+PyMODINIT_FUNC PyInit_csamtools(void); /*proto*/
+PyMODINIT_FUNC PyInit_csamtools(void)
+#endif
+{
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
+ __Pyx_RefNannyDeclarations
+ #if CYTHON_REFNANNY
+ __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
+ if (!__Pyx_RefNanny) {
+ PyErr_Clear();
+ __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
+ if (!__Pyx_RefNanny)
+ Py_FatalError("failed to import 'refnanny' module");
+ }
+ #endif
+ __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", 0);
+ if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __Pyx_CyFunction_USED
+ if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ #ifdef __Pyx_FusedFunction_USED
+ if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ #ifdef __Pyx_Generator_USED
+ if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ /*--- Library function declarations ---*/
+ /*--- Threads initialization code ---*/
+ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
+ #ifdef WITH_THREAD /* Python build with threading support? */
+ PyEval_InitThreads();
+ #endif
+ #endif
+ /*--- Module creation code ---*/
+ #if PY_MAJOR_VERSION < 3
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ #else
+ __pyx_m = PyModule_Create(&__pyx_moduledef);
+ #endif
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ /*--- Initialize various global constants etc. ---*/
+ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_module_is_main_csamtools) {
+ if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ }
+ /*--- Builtin init code ---*/
+ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Constants init code ---*/
+ if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Global init code ---*/
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ /*--- Variable export code ---*/
+ /*--- Function export code ---*/
+ /*--- Type init code ---*/
+ __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
+ __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
+ if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
+ if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_9csamtools_11AlignedRead_4__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_4__str__;
+ }
+ }
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
+ __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
+ __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
+ __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
+ __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
+ __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
+ __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
+ if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_7Samfile_42__next__.doc = __pyx_doc_9csamtools_7Samfile_42__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_42__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
+ __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
+ __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
+ __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
+ __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
+ __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
+ __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
+ __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__;
+ }
+ }
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
+ __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
+ __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
+ __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
+ __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
+ __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
+ __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
+ __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
+ __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
+ __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
+ __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
+ __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
+ __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion;
+ __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs;
+ __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
+ __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs;
+ if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IndexedReads = &__pyx_type_9csamtools_IndexedReads;
+ if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
+ if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_9csamtools___pyx_scope_struct__genexpr;
+ if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_9csamtools___pyx_scope_struct_1_genexpr;
+ /*--- Type import code ---*/
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Variable import code ---*/
+ /*--- Function import code ---*/
+ /*--- Execution code ---*/
- /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1
- * # cython: embedsignature=True # <<<<<<<<<<<<<<
+ /* "csamtools.pyx":4
* # cython: profile=True
* # adds doc-strings for sphinx
+ * import tempfile # <<<<<<<<<<<<<<
+ * import os
+ * import sys
*/
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Fastafile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_177), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Fastafile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___open); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_178), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Fastafile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fetch); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_179), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_180), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_181), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___open); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_182), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__gettid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_183), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__getrname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_184), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_185), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__seek); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_186), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__tell); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_187), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fetch); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_188), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__mate); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_189), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tempfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":5
+ * # adds doc-strings for sphinx
+ * import tempfile
+ * import os # <<<<<<<<<<<<<<
+ * import sys
+ * import types
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__os), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__count); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__os, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":6
+ * import tempfile
+ * import os
+ * import sys # <<<<<<<<<<<<<<
+ * import types
+ * import itertools
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_190), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sys, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":7
+ * import os
+ * import sys
+ * import types # <<<<<<<<<<<<<<
+ * import itertools
+ * import struct
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__types), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__pileup); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__types, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":8
+ * import sys
+ * import types
+ * import itertools # <<<<<<<<<<<<<<
+ * import struct
+ * import ctypes
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__itertools), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_191), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__itertools, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":9
+ * import types
+ * import itertools
+ * import struct # <<<<<<<<<<<<<<
+ * import ctypes
+ * import collections
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__struct), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__close); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__struct, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":10
+ * import itertools
+ * import struct
+ * import ctypes # <<<<<<<<<<<<<<
+ * import collections
+ * import re
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__ctypes), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_192), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__ctypes, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":11
+ * import struct
+ * import ctypes
+ * import collections # <<<<<<<<<<<<<<
+ * import re
+ * import platform
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__collections), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__write); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__collections, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":12
+ * import ctypes
+ * import collections
+ * import re # <<<<<<<<<<<<<<
+ * import platform
+ * import warnings
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__re), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_193), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__re, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":13
+ * import collections
+ * import re
+ * import platform # <<<<<<<<<<<<<<
+ * import warnings
+ * from cpython cimport PyErr_SetString, PyBytes_Check, PyUnicode_Check, PyBytes_FromStringAndSize
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__platform), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s___buildLine); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__platform, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":14
+ * import re
+ * import platform
+ * import warnings # <<<<<<<<<<<<<<
+ * from cpython cimport PyErr_SetString, PyBytes_Check, PyUnicode_Check, PyBytes_FromStringAndSize
+ * from cpython.version cimport PY_MAJOR_VERSION
+ */
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__warnings), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_194), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__warnings, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Samfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":23
+ * ## Python 3 compatibility functions
+ * ########################################################################
+ * IS_PYTHON3 = PY_MAJOR_VERSION >= 3 # <<<<<<<<<<<<<<
+ * cdef from_string_and_size(char* s, size_t length):
+ * if PY_MAJOR_VERSION < 3:
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong((PY_MAJOR_VERSION >= 3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__IS_PYTHON3, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":32
+ * # filename encoding (copied from lxml.etree.pyx)
+ * cdef str _FILENAME_ENCODING
+ * _FILENAME_ENCODING = sys.getfilesystemencoding() # <<<<<<<<<<<<<<
+ * if _FILENAME_ENCODING is None:
+ * _FILENAME_ENCODING = sys.getdefaultencoding()
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_195), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s_249); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorRowRegion); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":33
+ * cdef str _FILENAME_ENCODING
+ * _FILENAME_ENCODING = sys.getfilesystemencoding()
+ * if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
+ * _FILENAME_ENCODING = sys.getdefaultencoding()
+ * if _FILENAME_ENCODING is None:
+ */
+ __pyx_t_3 = (__pyx_v_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
+ if (__pyx_t_3) {
+
+ /* "csamtools.pyx":34
+ * _FILENAME_ENCODING = sys.getfilesystemencoding()
+ * if _FILENAME_ENCODING is None:
+ * _FILENAME_ENCODING = sys.getdefaultencoding() # <<<<<<<<<<<<<<
+ * if _FILENAME_ENCODING is None:
+ * _FILENAME_ENCODING = 'ascii'
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__getdefaultencoding); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_t_1 = 0;
+ goto __pyx_L2;
+ }
+ __pyx_L2:;
+
+ /* "csamtools.pyx":35
+ * if _FILENAME_ENCODING is None:
+ * _FILENAME_ENCODING = sys.getdefaultencoding()
+ * if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
+ * _FILENAME_ENCODING = 'ascii'
+ *
+ */
+ __pyx_t_3 = (__pyx_v_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
+ if (__pyx_t_3) {
+
+ /* "csamtools.pyx":36
+ * _FILENAME_ENCODING = sys.getdefaultencoding()
+ * if _FILENAME_ENCODING is None:
+ * _FILENAME_ENCODING = 'ascii' # <<<<<<<<<<<<<<
+ *
+ * #cdef char* _C_FILENAME_ENCODING
+ */
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __pyx_v_9csamtools__FILENAME_ENCODING = __pyx_n_s__ascii;
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "csamtools.pyx":138
+ * DEF BAM_CDIFF = 8
+ *
+ * cdef char* CODE2CIGAR= "MIDNSHP=X" # <<<<<<<<<<<<<<
+ * if IS_PYTHON3:
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ */
+ __pyx_v_9csamtools_CODE2CIGAR = __pyx_k_250;
+
+ /* "csamtools.pyx":139
+ *
+ * cdef char* CODE2CIGAR= "MIDNSHP=X"
+ * if IS_PYTHON3: # <<<<<<<<<<<<<<
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__IS_PYTHON3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_196), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorRowAll); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
+
+ /* "csamtools.pyx":140
+ * cdef char* CODE2CIGAR= "MIDNSHP=X"
+ * if IS_PYTHON3:
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
+ */
+ __pyx_t_1 = __pyx_pf_9csamtools_2genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyDict_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CIGAR2CODE, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L4;
+ }
+ /*else*/ {
+
+ /* "csamtools.pyx":142
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+ *
+ */
+ __pyx_t_1 = __pyx_pf_9csamtools_5genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyDict_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CIGAR2CODE, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ }
+ __pyx_L4:;
+
+ /* "csamtools.pyx":143
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) # <<<<<<<<<<<<<<
+ *
+ * #####################################################################
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_252), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_197), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CIGAR_REGEX, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorRowAllRefs); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":147
+ * #####################################################################
+ * ## set pysam stderr to /dev/null
+ * pysam_unset_stderr() # <<<<<<<<<<<<<<
+ *
+ * #####################################################################
+ */
+ pysam_unset_stderr();
+
+ /* "csamtools.pyx":151
+ * #####################################################################
+ * # hard-coded constants
+ * cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN" # <<<<<<<<<<<<<<
+ * cdef int max_pos = 2 << 29
+ *
+ */
+ __pyx_v_9csamtools_bam_nt16_rev_table = __pyx_k_253;
+
+ /* "csamtools.pyx":152
+ * # hard-coded constants
+ * cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN"
+ * cdef int max_pos = 2 << 29 # <<<<<<<<<<<<<<
+ *
+ * #####################################################################
+ */
+ __pyx_v_9csamtools_max_pos = 1073741824;
+
+ /* "csamtools.pyx":247
+ * (<object>f)(a)
+ *
+ * class PileupColumn(object): # <<<<<<<<<<<<<<
+ * '''A pileup column. A pileup column contains
+ * all the reads that map to a certain target base.
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+
+ /* "csamtools.pyx":260
+ * list of reads (:class:`pysam.PileupRead`) aligned to this column
+ * '''
+ * def __str__(self): # <<<<<<<<<<<<<<
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" + "\n".join( map(str, self.pileups) )
+ */
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_12PileupColumn_1__str__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_255)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____str__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+
+ /* "csamtools.pyx":247
+ * (<object>f)(a)
+ *
+ * class PileupColumn(object): # <<<<<<<<<<<<<<
+ * '''A pileup column. A pileup column contains
+ * all the reads that map to a certain target base.
+ */
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_builtin_object);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_object);
+ __Pyx_GIVEREF(__pyx_builtin_object);
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_257)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PileupColumn, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_198), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s_200); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":304
+ * return 0
+ *
+ * class StderrStore(): # <<<<<<<<<<<<<<
+ * '''
+ * stderr is captured.
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+
+ /* "csamtools.pyx":308
+ * stderr is captured.
+ * '''
+ * def __init__(self): # <<<<<<<<<<<<<<
+ * return
+ * self.stderr_h, self.stderr_f = tempfile.mkstemp()
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_199), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorColumn); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__addReference); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":314
+ * self.stderr_save.setfd( self.stderr_h )
+ *
+ * def readAndRelease( self ): # <<<<<<<<<<<<<<
+ * return []
+ * self.stderr_save.restore()
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3readAndRelease, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_261)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_201), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorColumn); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__hasReference); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":323
+ * return lines
+ *
+ * def release(self): # <<<<<<<<<<<<<<
+ * return
+ * self.stderr_save.restore()
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_5release, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_263)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_202), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s_204); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":329
+ * os.remove( self.stderr_f )
+ *
+ * def __del__(self): # <<<<<<<<<<<<<<
+ * self.release()
+ *
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_7__del__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_265)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____del__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_203), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s_206); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____next__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":304
+ * return 0
+ *
+ * class StderrStore(): # <<<<<<<<<<<<<<
+ * '''
+ * stderr is captured.
+ */
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_266)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_205), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__AlignedRead); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____str__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":332
+ * self.release()
+ *
+ * class StderrStoreWindows(): # <<<<<<<<<<<<<<
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+
+ /* "csamtools.pyx":334
+ * class StderrStoreWindows():
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass # <<<<<<<<<<<<<<
+ * def readAndRelease(self): return []
+ * def release(self): pass
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_268)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_207), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__AlignedRead); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compare); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":335
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass
+ * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
+ * def release(self): pass
+ *
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_3readAndRelease, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_270)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_208), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__AlignedRead); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__overlap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":336
+ * def __init__(self): pass
+ * def readAndRelease(self): return []
+ * def release(self): pass # <<<<<<<<<<<<<<
+ *
+ * if platform.system()=='Windows':
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_5release, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_272)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_209), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__AlignedRead); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__opt); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":332
+ * self.release()
+ *
+ * class StderrStoreWindows(): # <<<<<<<<<<<<<<
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass
+ */
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_273)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStoreWindows, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_210), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__AlignedRead); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":338
+ * def release(self): pass
+ *
+ * if platform.system()=='Windows': # <<<<<<<<<<<<<<
+ * del StderrStore
+ * StderrStore = StderrStoreWindows
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__platform); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fancy_str); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__system); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_211), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Windows), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
+
+ /* "csamtools.pyx":339
+ *
+ * if platform.system()=='Windows':
+ * del StderrStore # <<<<<<<<<<<<<<
+ * StderrStore = StderrStoreWindows
+ *
+ */
+ if (__Pyx_DelAttrString(__pyx_m, "StderrStore") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":340
+ * if platform.system()=='Windows':
+ * del StderrStore
+ * StderrStore = StderrStoreWindows # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStoreWindows); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L5;
+ }
+ __pyx_L5:;
+
+ /* "csamtools.pyx":347
+ * ######################################################################
+ * # valid types for sam headers
+ * VALID_HEADER_TYPES = { "HD" : dict, # <<<<<<<<<<<<<<
+ * "SQ" : list,
+ * "RG" : list,
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)(&PyDict_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":348
+ * # valid types for sam headers
+ * VALID_HEADER_TYPES = { "HD" : dict,
+ * "SQ" : list, # <<<<<<<<<<<<<<
+ * "RG" : list,
+ * "PG" : list,
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":349
+ * VALID_HEADER_TYPES = { "HD" : dict,
+ * "SQ" : list,
+ * "RG" : list, # <<<<<<<<<<<<<<
+ * "PG" : list,
+ * "CO" : list }
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":350
+ * "SQ" : list,
+ * "RG" : list,
+ * "PG" : list, # <<<<<<<<<<<<<<
+ * "CO" : list }
+ *
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":351
+ * "RG" : list,
+ * "PG" : list,
+ * "CO" : list } # <<<<<<<<<<<<<<
+ *
+ * # order of records within sam headers
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":354
+ *
+ * # order of records within sam headers
+ * VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<<
+ *
+ * # type conversions within sam header records
+ */
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_274)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":357
+ *
+ * # type conversions within sam header records
+ * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, # <<<<<<<<<<<<<<
+ * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
+ * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+
+ /* "csamtools.pyx":358
+ * # type conversions within sam header records
+ * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
+ * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, # <<<<<<<<<<<<<<
+ * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
+ */
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)(&PyInt_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+
+ /* "csamtools.pyx":359
+ * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
+ * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
+ * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, # <<<<<<<<<<<<<<
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
+ * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
+ */
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":360
+ * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
+ * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, # <<<<<<<<<<<<<<
+ * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
+ *
+ */
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+
+ /* "csamtools.pyx":361
+ * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
+ * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } # <<<<<<<<<<<<<<
+ *
+ * # output order of fields within records
+ */
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":364
+ *
+ * # output order of fields within records
+ * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
+ * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_275)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":365
+ * # output order of fields within records
+ * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
+ * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
+ * "PG" : ( "PN", "ID", "VN", "CL" ), }
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_276)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":366
+ * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
+ * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), # <<<<<<<<<<<<<<
+ * "PG" : ( "PN", "ID", "VN", "CL" ), }
+ *
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_277)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":367
+ * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
+ * "PG" : ( "PN", "ID", "VN", "CL" ), } # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_278)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":619
+ * header = None,
+ * port = None,
+ * add_sq_text = True, # <<<<<<<<<<<<<<
+ * check_header = True,
+ * check_sq = True,
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__setdevice); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_21 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":620
+ * port = None,
+ * add_sq_text = True,
+ * check_header = True, # <<<<<<<<<<<<<<
+ * check_sq = True,
+ * ):
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_212), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_22 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":621
+ * add_sq_text = True,
+ * check_header = True,
+ * check_sq = True, # <<<<<<<<<<<<<<
+ * ):
+ * '''open a sam/bam file.
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__setfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_23 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":900
+ * region = None,
+ * callback = None,
+ * until_eof = False ): # <<<<<<<<<<<<<<
+ * '''
+ * fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_213), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_54 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":1020
+ * end = None,
+ * region = None,
+ * until_eof = False ): # <<<<<<<<<<<<<<
+ * '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
+ *
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__restore); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_73 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":1937
+ * int tid = 0,
+ * int start = 0,
+ * int end = max_pos, # <<<<<<<<<<<<<<
+ * int truncate = False,
+ * **kwargs ):
+ */
+ __pyx_k_128 = __pyx_v_9csamtools_max_pos;
+
+ /* "csamtools.pyx":3090
+ * return self._level
+ *
+ * class Outs: # <<<<<<<<<<<<<<
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1):
+ */
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+
+ /* "csamtools.pyx":3092
+ * class Outs:
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1): # <<<<<<<<<<<<<<
+ * self.streams = []
+ * self.id = id
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_280)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetAttrString(__pyx_t_4, "__doc__"); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_4, ((PyObject *)__pyx_k_tuple_281));
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_214), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_m, __pyx_n_s___samtools_dispatch); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_GetAttrString(__pyx_t_1, "__doc__"); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3096
+ * self.id = id
+ *
+ * def setdevice(self, filename): # <<<<<<<<<<<<<<
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_3setdevice, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_283)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_215), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setdevice, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorSNPCalls); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3101
+ * self.setfd(fd)
+ *
+ * def setfile(self, filename): # <<<<<<<<<<<<<<
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_5setfile, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_285)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s____next__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfile, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetAttrString(__pyx_t_1, "__doc__"); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3106
+ * self.setfd(fd)
+ *
+ * def setfd(self, fd): # <<<<<<<<<<<<<<
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_7setfd, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_287)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_216), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfd, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_m, __pyx_n_s__SNPCaller); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3114
+ * os.close(fd) # Close other unit (look out, caller.)
+ *
+ * def restore(self): # <<<<<<<<<<<<<<
+ * '''restore previous output stream'''
+ * if self.streams:
+ */
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_9restore, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_289)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__call); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__restore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetAttrString(__pyx_t_1, "__doc__"); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3090
+ * return self._level
+ *
+ * class Outs: # <<<<<<<<<<<<<<
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1):
+ */
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_290)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__Outs, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_217), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IndelCaller); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__call); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":3127
+ * def _samtools_dispatch( method,
+ * args = (),
+ * catch_stdout = True ): # <<<<<<<<<<<<<<
+ * '''call ``method`` in samtools providing arguments in args.
+ *
+ */
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetAttrString(__pyx_t_1, "__doc__"); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_218), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IteratorIndelCalls); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s____next__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_176 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+
+ /* "csamtools.pyx":3125
+ * del self.streams[-1]
+ *
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
+ * args = (),
+ * catch_stdout = True ):
+ */
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetAttrString(__pyx_t_1, "__doc__"); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_219), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_m, __pyx_n_s__IndexedReads); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__build); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":3836
+ * if self.owns_samfile: samclose( self.fp )
+ *
+ * __all__ = ["Samfile", # <<<<<<<<<<<<<<
+ * "Fastafile",
+ * "IteratorRow",
+ */
+ __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetAttrString(__pyx_t_1, "__doc__"); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_220), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Samfile));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__Fastafile));
+ PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__Fastafile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Fastafile));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorRow));
+ PyList_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__IteratorRow));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorRow));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorColumn));
+ PyList_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__IteratorColumn));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorColumn));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__AlignedRead));
+ PyList_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__AlignedRead));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__AlignedRead));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__PileupColumn));
+ PyList_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__PileupColumn));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupColumn));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__PileupProxy));
+ PyList_SET_ITEM(__pyx_t_1, 6, ((PyObject *)__pyx_n_s__PileupProxy));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupProxy));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__PileupRead));
+ PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__PileupRead));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupRead));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__IndexedReads));
+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__IndexedReads));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndexedReads));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "/ifs/apps/apps/python-2.7.1/lib/python2.7/site-packages/Cython-0.13-py2.7-linux-x86_64.egg/Cython/Includes/cpython/type.pxd":2
- *
- * cdef extern from "Python.h": # <<<<<<<<<<<<<<
- * # The C structure of the objects used to describe built-in types.
- *
+ /* "csamtools.pyx":1
+ * # cython: embedsignature=True # <<<<<<<<<<<<<<
+ * # cython: profile=True
+ * # adds doc-strings for sphinx
*/
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
if (__pyx_m) {
- __Pyx_AddTraceback("init csamtools");
+ __Pyx_AddTraceback("init csamtools", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
PyErr_SetString(PyExc_ImportError, "init csamtools");
}
/* Runtime support code */
+#if CYTHON_REFNANNY
+static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
+ PyObject *m = NULL, *p = NULL;
+ void *r = NULL;
+ m = PyImport_ImportModule((char *)modname);
+ if (!m) goto end;
+ p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
+ if (!p) goto end;
+ r = PyLong_AsVoidPtr(p);
+end:
+ Py_XDECREF(p);
+ Py_XDECREF(m);
+ return (__Pyx_RefNannyAPIStruct *)r;
+}
+#endif /* CYTHON_REFNANNY */
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
PyObject *result;
result = PyObject_GetAttr(dict, name);
- if (!result)
- PyErr_SetObject(PyExc_NameError, name);
+ if (!result) {
+ if (dict != __pyx_b) {
+ PyErr_Clear();
+ result = PyObject_GetAttr(__pyx_b, name);
+ }
+ if (!result) {
+ PyErr_SetObject(PyExc_NameError, name);
+ }
+ }
return result;
}
-
#if CYTHON_PROFILE
-
static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
PyFrameObject** frame,
const char *funcname,
}
return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
}
-
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
PyCodeObject *py_code = 0;
-
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
py_srcfile = PyString_FromString(srcfile);
py_srcfile = PyUnicode_FromString(srcfile);
#endif
if (!py_funcname | !py_srcfile) goto bad;
-
py_code = PyCode_New(
0, /*int argcount,*/
#if PY_MAJOR_VERSION >= 3
firstlineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
-
-bad:
+bad:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
-
return py_code;
}
-
#endif /* CYTHON_PROFILE */
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_Restore(type, value, tb);
+#endif
}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "need more than %d value%s to unpack", (int)index,
- #else
- "need more than %zd value%s to unpack", index,
- #endif
- (index == 1) ? "" : "s");
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(type, value, tb);
+#endif
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ Py_DECREF(value);
+ value = type;
#if PY_VERSION_HEX < 0x02050000
- "too many values to unpack (expected %d)", (int)expected);
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
#else
- "too many values to unpack (expected %zd)", expected);
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
#endif
+ }
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
}
-
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
- PyObject *item;
- if (!(item = PyIter_Next(iter))) {
- if (!PyErr_Occurred()) {
- __Pyx_RaiseNeedMoreValuesError(index);
+#else /* Python 3+ */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+ if (cause) {
+ PyObject *fixed_cause;
+ if (PyExceptionClass_Check(cause)) {
+ fixed_cause = PyObject_CallObject(cause, NULL);
+ if (fixed_cause == NULL)
+ goto bad;
+ }
+ else if (PyExceptionInstance_Check(cause)) {
+ fixed_cause = cause;
+ Py_INCREF(fixed_cause);
+ }
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "exception causes must derive from "
+ "BaseException");
+ goto bad;
+ }
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
+ PyException_SetCause(value, fixed_cause);
+ }
+ PyErr_SetObject(type, value);
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
}
}
- return item;
+bad:
+ return;
}
+#endif
-static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
- PyObject *item;
- if ((item = PyIter_Next(iter))) {
- Py_DECREF(item);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- }
- else if (!PyErr_Occurred())
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
+ if (unlikely(!type)) {
+ PyErr_Format(PyExc_SystemError, "Missing type object");
return 0;
- else
- return -1;
+ }
+ if (likely(PyObject_TypeCheck(obj, type)))
+ return 1;
+ PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
+ Py_TYPE(obj)->tp_name, type->tp_name);
+ return 0;
}
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
#else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
+ if (unlikely(!PyUnicode_Check(key)))
#endif
goto invalid_keyword_type;
}
#endif
}
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *number, *more_or_less;
-
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- number = (num_expected == 1) ? "" : "s";
- PyErr_Format(PyExc_TypeError,
- #if PY_VERSION_HEX < 0x02050000
- "%s() takes %s %d positional argument%s (%d given)",
- #else
- "%s() takes %s %zd positional argument%s (%zd given)",
- #endif
- func_name, more_or_less, num_expected, number, num_found);
-}
-
static int __Pyx_ParseOptionalKeywords(
PyObject *kwds,
PyObject **argnames[],
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
-
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
#else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+ if (unlikely(!PyUnicode_Check(key))) {
#endif
goto invalid_keyword_type;
} else {
if (*name) {
values[name-argnames] = value;
} else {
- /* unexpected keyword found */
for (name=argnames; name != first_kw_arg; name++) {
if (**name == key) goto arg_passed_twice;
#if PY_MAJOR_VERSION >= 3
return -1;
}
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *more_or_less;
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ PyErr_Format(PyExc_TypeError,
+ "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ func_name, more_or_less, num_expected,
+ (num_expected == 1) ? "" : "s", num_found);
}
-
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact)
{
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ index, (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+}
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ } else if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
}
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
return r;
}
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
+ PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
+}
+
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
Py_XINCREF(*value);
Py_XINCREF(*tb);
}
-
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
Py_XDECREF(tmp_tb);
}
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
- PyObject *py_import = 0;
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
+ PyObject *py_import = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
+ if (!py_import)
+ goto bad;
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ #if PY_VERSION_HEX >= 0x02050000
+ {
+ #if PY_MAJOR_VERSION >= 3
+ if (level == -1) {
+ if (strchr(__Pyx_MODULE_NAME, '.')) {
+ /* try package relative import first */
+ PyObject *py_level = PyInt_FromLong(1);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ if (!module) {
+ if (!PyErr_ExceptionMatches(PyExc_ImportError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ level = 0; /* try absolute import on failure */
+ }
+ #endif
+ if (!module) {
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ }
+ }
+ #else
+ if (level>0) {
+ PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
+ goto bad;
+ }
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+ #endif
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(py_import);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
+ PyObject *metaclass;
+ /* Default metaclass */
+#if PY_MAJOR_VERSION < 3
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = PyObject_GetAttrString(base, (char *)"__class__");
+ if (!metaclass) {
+ PyErr_Clear();
+ metaclass = (PyObject*) Py_TYPE(base);
+ }
+ } else {
+ metaclass = (PyObject *) &PyClass_Type;
+ }
+#else
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = (PyObject*) Py_TYPE(base);
+ } else {
+ metaclass = (PyObject *) &PyType_Type;
+ }
+#endif
+ Py_INCREF(metaclass);
+ return metaclass;
+}
+
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname) {
+ PyObject *result;
+ PyObject *metaclass;
+ if (PyDict_SetItemString(dict, "__module__", modname) < 0)
+ return NULL;
+ /* Python2 __metaclass__ */
+ metaclass = PyDict_GetItemString(dict, "__metaclass__");
+ if (metaclass) {
+ Py_INCREF(metaclass);
+ } else {
+ metaclass = __Pyx_FindPy2Metaclass(bases);
+ }
+ result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
+ Py_DECREF(metaclass);
+ return result;
+}
+
+static PyObject *
+__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
+{
+ if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
+#if PY_MAJOR_VERSION >= 3
+ op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
+#else
+ op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
+#endif
+ }
+ if (op->func_doc == 0) {
+ Py_INCREF(Py_None);
+ return Py_None;
+ }
+ Py_INCREF(op->func_doc);
+ return op->func_doc;
+}
+static int
+__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp = op->func_doc;
+ if (value == NULL)
+ op->func_doc = Py_None; /* Mark as deleted */
+ else
+ op->func_doc = value;
+ Py_INCREF(op->func_doc);
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
+{
+ if (op->func_name == NULL) {
+#if PY_MAJOR_VERSION >= 3
+ op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
+#else
+ op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
+#endif
+ }
+ Py_INCREF(op->func_name);
+ return op->func_name;
+}
+static int
+__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+ if (value == NULL || !PyUnicode_Check(value)) {
+#else
+ if (value == NULL || !PyString_Check(value)) {
+#endif
+ PyErr_SetString(PyExc_TypeError,
+ "__name__ must be set to a string object");
+ return -1;
+ }
+ tmp = op->func_name;
+ Py_INCREF(value);
+ op->func_name = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
+{
+ PyObject *self;
+ self = m->func_closure;
+ if (self == NULL)
+ self = Py_None;
+ Py_INCREF(self);
+ return self;
+}
+static PyObject *
+__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
+{
+ if (op->func_dict == NULL) {
+ op->func_dict = PyDict_New();
+ if (op->func_dict == NULL)
+ return NULL;
+ }
+ Py_INCREF(op->func_dict);
+ return op->func_dict;
+}
+static int
+__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+ if (value == NULL) {
+ PyErr_SetString(PyExc_TypeError,
+ "function's dictionary may not be deleted");
+ return -1;
+ }
+ if (!PyDict_Check(value)) {
+ PyErr_SetString(PyExc_TypeError,
+ "setting function's dictionary to a non-dict");
+ return -1;
+ }
+ tmp = op->func_dict;
+ Py_INCREF(value);
+ op->func_dict = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+ PyObject* dict = PyModule_GetDict(__pyx_m);
+ Py_XINCREF(dict);
+ return dict;
+}
+static PyObject *
+__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+static PyObject *
+__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
+{
+ PyObject* result = (op->func_code) ? op->func_code : Py_None;
+ Py_INCREF(result);
+ return result;
+}
+static PyObject *
+__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
+{
+ if (op->defaults_tuple) {
+ Py_INCREF(op->defaults_tuple);
+ return op->defaults_tuple;
+ }
+ if (op->defaults_getter) {
+ PyObject *res = op->defaults_getter((PyObject *) op);
+ if (res) {
+ Py_INCREF(res);
+ op->defaults_tuple = res;
+ }
+ return res;
+ }
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+static PyGetSetDef __pyx_CyFunction_getsets[] = {
+ {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+ {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+ {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
+ {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+ {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+ {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+ {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+ {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+ {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+ {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+ {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+ {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+ {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
+#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
+#endif
+static PyMemberDef __pyx_CyFunction_members[] = {
+ {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
+ {0, 0, 0, 0, 0}
+};
+static PyObject *
+__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
+{
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_FromString(m->func.m_ml->ml_name);
+#else
+ return PyString_FromString(m->func.m_ml->ml_name);
+#endif
+}
+static PyMethodDef __pyx_CyFunction_methods[] = {
+ {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
+ {0, 0, 0, 0}
+};
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
+ PyObject *closure, PyObject *module, PyObject* code) {
+ __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
+ if (op == NULL)
+ return NULL;
+ op->flags = flags;
+ op->func_weakreflist = NULL;
+ op->func.m_ml = ml;
+ op->func.m_self = (PyObject *) op;
+ Py_XINCREF(closure);
+ op->func_closure = closure;
+ Py_XINCREF(module);
+ op->func.m_module = module;
+ op->func_dict = NULL;
+ op->func_name = NULL;
+ op->func_doc = NULL;
+ op->func_classobj = NULL;
+ Py_XINCREF(code);
+ op->func_code = code;
+ op->defaults_pyobjects = 0;
+ op->defaults = NULL;
+ op->defaults_tuple = NULL;
+ op->defaults_getter = NULL;
+ PyObject_GC_Track(op);
+ return (PyObject *) op;
+}
+static int
+__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
+{
+ Py_CLEAR(m->func_closure);
+ Py_CLEAR(m->func.m_module);
+ Py_CLEAR(m->func_dict);
+ Py_CLEAR(m->func_name);
+ Py_CLEAR(m->func_doc);
+ Py_CLEAR(m->func_code);
+ Py_CLEAR(m->func_classobj);
+ Py_CLEAR(m->defaults_tuple);
+ if (m->defaults) {
+ PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+ int i;
+ for (i = 0; i < m->defaults_pyobjects; i++)
+ Py_XDECREF(pydefaults[i]);
+ PyMem_Free(m->defaults);
+ m->defaults = NULL;
+ }
+ return 0;
+}
+static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
+{
+ PyObject_GC_UnTrack(m);
+ if (m->func_weakreflist != NULL)
+ PyObject_ClearWeakRefs((PyObject *) m);
+ __Pyx_CyFunction_clear(m);
+ PyObject_GC_Del(m);
+}
+static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
+{
+ Py_VISIT(m->func_closure);
+ Py_VISIT(m->func.m_module);
+ Py_VISIT(m->func_dict);
+ Py_VISIT(m->func_name);
+ Py_VISIT(m->func_doc);
+ Py_VISIT(m->func_code);
+ Py_VISIT(m->func_classobj);
+ Py_VISIT(m->defaults_tuple);
+ if (m->defaults) {
+ PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+ int i;
+ for (i = 0; i < m->defaults_pyobjects; i++)
+ Py_VISIT(pydefaults[i]);
+ }
+ return 0;
+}
+static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
+{
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
+ Py_INCREF(func);
+ return func;
+ }
+ if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
+ if (type == NULL)
+ type = (PyObject *)(Py_TYPE(obj));
+ return PyMethod_New(func,
+ type, (PyObject *)(Py_TYPE(type)));
+ }
+ if (obj == Py_None)
+ obj = NULL;
+ return PyMethod_New(func, obj, type);
+}
+static PyObject*
+__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
+{
+ PyObject *func_name = __Pyx_CyFunction_get_name(op);
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_FromFormat("<cyfunction %U at %p>",
+ func_name, (void *)op);
+#else
+ return PyString_FromFormat("<cyfunction %s at %p>",
+ PyString_AsString(func_name), (void *)op);
+#endif
+}
+static PyTypeObject __pyx_CyFunctionType_type = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
+ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+#if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+#else
+ 0, /*reserved*/
+#endif
+ (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ __Pyx_PyCFunction_Call, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
+ 0, /*tp_doc*/
+ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
+ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_CyFunction_methods, /*tp_methods*/
+ __pyx_CyFunction_members, /*tp_members*/
+ __pyx_CyFunction_getsets, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ __Pyx_CyFunction_descr_get, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ 0, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+#endif
+};
+static int __Pyx_CyFunction_init(void)
+{
+ if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+ return -1;
+ __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
+ return 0;
+}
+void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
+{
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ m->defaults = PyMem_Malloc(size);
+ if (!m->defaults)
+ return PyErr_NoMemory();
+ memset(m->defaults, 0, sizeof(size));
+ m->defaults_pyobjects = pyobjects;
+ return m->defaults;
+}
+static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
+{
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ m->defaults_tuple = tuple;
+ Py_INCREF(tuple);
+}
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyBytes_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+ else
+ return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+ } else {
+ int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
+ #if CYTHON_PEP393_ENABLED
+ if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
+ return -1;
+ if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_LENGTH(s1) == 1) {
+ Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
+ Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #else
+ if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_SIZE(s1) == 1) {
+ Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
+ Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #endif
+ } else {
+ int result = PyUnicode_Compare(s1, s2);
+ if ((result == -1) && unlikely(PyErr_Occurred()))
+ return -1;
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t val) {
+ const int8_t neg_one = (int8_t)-1, const_zero = (int8_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(int8_t) == sizeof(char)) ||
+ (sizeof(int8_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(int8_t) == sizeof(int)) ||
+ (sizeof(int8_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(int8_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(int8_t),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) {
+ const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(uint8_t) == sizeof(char)) ||
+ (sizeof(uint8_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(uint8_t) == sizeof(int)) ||
+ (sizeof(uint8_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(uint8_t),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int16_t(int16_t val) {
+ const int16_t neg_one = (int16_t)-1, const_zero = (int16_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(int16_t) == sizeof(char)) ||
+ (sizeof(int16_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(int16_t) == sizeof(int)) ||
+ (sizeof(int16_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(int16_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(int16_t),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint16_t(uint16_t val) {
+ const uint16_t neg_one = (uint16_t)-1, const_zero = (uint16_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(uint16_t) == sizeof(char)) ||
+ (sizeof(uint16_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(uint16_t) == sizeof(int)) ||
+ (sizeof(uint16_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(uint16_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(uint16_t),
+ little, !is_unsigned);
}
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
-bad:
- Py_XDECREF(empty_list);
- Py_XDECREF(py_import);
- Py_XDECREF(empty_dict);
- return module;
}
-static PyObject *__Pyx_CreateClass(
- PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
-{
- PyObject *py_modname;
- PyObject *result = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_modname = PyString_FromString(modname);
- #else
- py_modname = PyUnicode_FromString(modname);
- #endif
- if (!py_modname)
- goto bad;
- if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- result = PyClass_New(bases, dict, name);
- #else
- result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
- #endif
-bad:
- Py_XDECREF(py_modname);
- return result;
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t val) {
+ const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(int32_t) == sizeof(char)) ||
+ (sizeof(int32_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(int32_t) == sizeof(int)) ||
+ (sizeof(int32_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(int32_t),
+ little, !is_unsigned);
+ }
}
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
} else {
int one = 1; int little = (int)*(unsigned char *)&one;
unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
+ return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
little, !is_unsigned);
}
}
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
const int is_unsigned = const_zero < neg_one;
}
}
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t val) {
- const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
+ const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
const int is_unsigned = const_zero < neg_one;
- if ((sizeof(int32_t) == sizeof(char)) ||
- (sizeof(int32_t) == sizeof(short))) {
+ if ((sizeof(int64_t) == sizeof(char)) ||
+ (sizeof(int64_t) == sizeof(short))) {
return PyInt_FromLong((long)val);
- } else if ((sizeof(int32_t) == sizeof(int)) ||
- (sizeof(int32_t) == sizeof(long))) {
+ } else if ((sizeof(int64_t) == sizeof(int)) ||
+ (sizeof(int64_t) == sizeof(long))) {
if (is_unsigned)
return PyLong_FromUnsignedLong((unsigned long)val);
else
return PyInt_FromLong((long)val);
- } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) {
+ } else if (sizeof(int64_t) == sizeof(PY_LONG_LONG)) {
if (is_unsigned)
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
else
} else {
int one = 1; int little = (int)*(unsigned char *)&one;
unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(int32_t),
+ return _PyLong_FromByteArray(bytes, sizeof(int64_t),
little, !is_unsigned);
}
}
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
- const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
+ const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
const int is_unsigned = const_zero < neg_one;
- if ((sizeof(int64_t) == sizeof(char)) ||
- (sizeof(int64_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(int64_t) == sizeof(int)) ||
- (sizeof(int64_t) == sizeof(long))) {
+ if (sizeof(uint64_t) == sizeof(char)) {
if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
+ return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
else
- return PyInt_FromLong((long)val);
- } else if (sizeof(int64_t) == sizeof(PY_LONG_LONG)) {
+ return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint64_t) == sizeof(short)) {
if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(int64_t),
- little, !is_unsigned);
+ return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint64_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint64_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint64_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint64_t)-1;
}
}
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
+static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
+ const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint64_t) == sizeof(char)) {
+ if (sizeof(uint8_t) == sizeof(char)) {
if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
+ return (uint8_t)__Pyx_PyInt_AsUnsignedChar(x);
else
- return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint64_t) == sizeof(short)) {
+ return (uint8_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint8_t) == sizeof(short)) {
if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
+ return (uint8_t)__Pyx_PyInt_AsUnsignedShort(x);
else
- return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint64_t) == sizeof(int)) {
+ return (uint8_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint8_t) == sizeof(int)) {
if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
+ return (uint8_t)__Pyx_PyInt_AsUnsignedInt(x);
else
- return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint64_t) == sizeof(long)) {
+ return (uint8_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint8_t) == sizeof(long)) {
if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
+ return (uint8_t)__Pyx_PyInt_AsUnsignedLong(x);
else
- return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ return (uint8_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) {
if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ return (uint8_t)__Pyx_PyInt_AsUnsignedLongLong(x);
else
- return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
+ return (uint8_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
- uint64_t val;
+ uint8_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
if (likely(v) && !PyLong_Check(v)) {
if (likely(!ret))
return val;
}
- return (uint64_t)-1;
+ return (uint8_t)-1;
}
}
}
}
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) {
- const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(uint8_t) == sizeof(char)) ||
- (sizeof(uint8_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(uint8_t) == sizeof(int)) ||
- (sizeof(uint8_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint8_t),
- little, !is_unsigned);
- }
-}
-
-#if PY_MAJOR_VERSION < 3
-static PyObject *__Pyx_GetStdout(void) {
- PyObject *f = PySys_GetObject((char *)"stdout");
- if (!f) {
- PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
- }
- return f;
-}
-
-static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) {
- PyObject* v;
- int i;
-
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
- if (PyFile_SoftSpace(f, 1)) {
- if (PyFile_WriteString(" ", f) < 0)
- return -1;
- }
- v = PyTuple_GET_ITEM(arg_tuple, i);
- if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
- return -1;
- if (PyString_Check(v)) {
- char *s = PyString_AsString(v);
- Py_ssize_t len = PyString_Size(v);
- if (len > 0 &&
- isspace(Py_CHARMASK(s[len-1])) &&
- s[len-1] != ' ')
- PyFile_SoftSpace(f, 0);
- }
- }
- if (newline) {
- if (PyFile_WriteString("\n", f) < 0)
- return -1;
- PyFile_SoftSpace(f, 0);
- }
- return 0;
-}
-
-#else /* Python 3 has a print function */
-
-static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
- PyObject* kwargs = 0;
- PyObject* result = 0;
- PyObject* end_string;
- if (unlikely(!__pyx_print)) {
- __pyx_print = __Pyx_GetAttrString(__pyx_b, "print");
- if (!__pyx_print)
- return -1;
- }
- if (stream) {
- kwargs = PyDict_New();
- if (unlikely(!kwargs))
- return -1;
- if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0))
- goto bad;
- if (!newline) {
- end_string = PyUnicode_FromStringAndSize(" ", 1);
- if (unlikely(!end_string))
- goto bad;
- if (PyDict_SetItemString(kwargs, "end", end_string) < 0) {
- Py_DECREF(end_string);
- goto bad;
- }
- Py_DECREF(end_string);
- }
- } else if (!newline) {
- if (unlikely(!__pyx_print_kwargs)) {
- __pyx_print_kwargs = PyDict_New();
- if (unlikely(!__pyx_print_kwargs))
- return -1;
- end_string = PyUnicode_FromStringAndSize(" ", 1);
- if (unlikely(!end_string))
- return -1;
- if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) {
- Py_DECREF(end_string);
- return -1;
- }
- Py_DECREF(end_string);
- }
- kwargs = __pyx_print_kwargs;
- }
- result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
- if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
- Py_DECREF(kwargs);
- if (!result)
- return -1;
- Py_DECREF(result);
- return 0;
-bad:
- if (kwargs != __pyx_print_kwargs)
- Py_XDECREF(kwargs);
- return -1;
-}
-
-#endif
-
-#if PY_MAJOR_VERSION < 3
-
-static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- if (PyFile_SoftSpace(f, 0)) {
- if (PyFile_WriteString(" ", f) < 0)
- return -1;
- }
- if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
- return -1;
- if (PyFile_WriteString("\n", f) < 0)
- return -1;
- return 0;
- /* the line below is just to avoid compiler
- * compiler warnings about unused functions */
- return __Pyx_Print(f, NULL, 0);
-}
-
-#else /* Python 3 has a print function */
-
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
- int res;
- PyObject* arg_tuple = PyTuple_New(1);
- if (unlikely(!arg_tuple))
- return -1;
- Py_INCREF(o);
- PyTuple_SET_ITEM(arg_tuple, 0, o);
- res = __Pyx_Print(stream, arg_tuple, 1);
- Py_DECREF(arg_tuple);
- return res;
-}
-
-#endif
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t val) {
const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
const int is_unsigned = const_zero < neg_one;
} else {
int one = 1; int little = (int)*(unsigned char *)&one;
unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint64_t),
+ return _PyLong_FromByteArray(bytes, sizeof(uint64_t),
little, !is_unsigned);
}
}
"can't convert negative value to unsigned long");
return (unsigned long)-1;
}
- return PyLong_AsUnsignedLong(x);
+ return (unsigned long)PyLong_AsUnsignedLong(x);
} else {
- return PyLong_AsLong(x);
+ return (unsigned long)PyLong_AsLong(x);
}
} else {
unsigned long val;
"can't convert negative value to unsigned PY_LONG_LONG");
return (unsigned PY_LONG_LONG)-1;
}
- return PyLong_AsUnsignedLongLong(x);
+ return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
- return PyLong_AsLongLong(x);
+ return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
unsigned PY_LONG_LONG val;
"can't convert negative value to long");
return (long)-1;
}
- return PyLong_AsUnsignedLong(x);
+ return (long)PyLong_AsUnsignedLong(x);
} else {
- return PyLong_AsLong(x);
+ return (long)PyLong_AsLong(x);
}
} else {
long val;
"can't convert negative value to PY_LONG_LONG");
return (PY_LONG_LONG)-1;
}
- return PyLong_AsUnsignedLongLong(x);
+ return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
- return PyLong_AsLongLong(x);
+ return (PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
PY_LONG_LONG val;
"can't convert negative value to signed long");
return (signed long)-1;
}
- return PyLong_AsUnsignedLong(x);
+ return (signed long)PyLong_AsUnsignedLong(x);
} else {
- return PyLong_AsLong(x);
+ return (signed long)PyLong_AsLong(x);
}
} else {
signed long val;
"can't convert negative value to signed PY_LONG_LONG");
return (signed PY_LONG_LONG)-1;
}
- return PyLong_AsUnsignedLongLong(x);
+ return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
- return PyLong_AsLongLong(x);
+ return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
signed PY_LONG_LONG val;
}
}
-static void __Pyx_WriteUnraisable(const char *name) {
+static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = *type;
+ tstate->exc_value = *value;
+ tstate->exc_traceback = *tb;
+ *type = tmp_type;
+ *value = tmp_value;
+ *tb = tmp_tb;
+}
+
+static PyObject *__Pyx_Generator_Next(PyObject *self);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
+static PyObject *__Pyx_Generator_Close(PyObject *self);
+static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
+static CYTHON_INLINE
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
+{
+ PyObject *exc_type = self->exc_type;
+ PyObject *exc_value = self->exc_value;
+ PyObject *exc_traceback = self->exc_traceback;
+ self->exc_type = NULL;
+ self->exc_value = NULL;
+ self->exc_traceback = NULL;
+ Py_XDECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_traceback);
+}
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
+{
+ PyObject *retval;
+ if (unlikely(self->is_running)) {
+ PyErr_SetString(PyExc_ValueError,
+ "generator already executing");
+ return NULL;
+ }
+ if (unlikely(self->resume_label == 0)) {
+ if (unlikely(value && value != Py_None)) {
+ PyErr_SetString(PyExc_TypeError,
+ "can't send non-None value to a "
+ "just-started generator");
+ return NULL;
+ }
+ }
+ if (unlikely(self->resume_label == -1)) {
+ PyErr_SetNone(PyExc_StopIteration);
+ return NULL;
+ }
+ if (value)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
+ __Pyx_Generator_ExceptionClear(self);
+ self->is_running = 1;
+ retval = self->body((PyObject *) self, value);
+ self->is_running = 0;
+ if (retval)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
+ __Pyx_Generator_ExceptionClear(self);
+ return retval;
+}
+static PyObject *__Pyx_Generator_Next(PyObject *self)
+{
+ return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
+}
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
+{
+ return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
+}
+static PyObject *__Pyx_Generator_Close(PyObject *self)
+{
+ __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ PyObject *retval;
+#if PY_VERSION_HEX < 0x02050000
+ PyErr_SetNone(PyExc_StopIteration);
+#else
+ PyErr_SetNone(PyExc_GeneratorExit);
+#endif
+ retval = __Pyx_Generator_SendEx(generator, NULL);
+ if (retval) {
+ Py_DECREF(retval);
+ PyErr_SetString(PyExc_RuntimeError,
+ "generator ignored GeneratorExit");
+ return NULL;
+ }
+#if PY_VERSION_HEX < 0x02050000
+ if (PyErr_ExceptionMatches(PyExc_StopIteration))
+#else
+ if (PyErr_ExceptionMatches(PyExc_StopIteration)
+ || PyErr_ExceptionMatches(PyExc_GeneratorExit))
+#endif
+ {
+ PyErr_Clear(); /* ignore these errors */
+ Py_INCREF(Py_None);
+ return Py_None;
+ }
+ return NULL;
+}
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
+{
+ __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ PyObject *typ;
+ PyObject *tb = NULL;
+ PyObject *val = NULL;
+ if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
+ return NULL;
+ __Pyx_Raise(typ, val, tb, NULL);
+ return __Pyx_Generator_SendEx(generator, NULL);
+}
+static int
+__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
+{
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_VISIT(gen->closure);
+ Py_VISIT(gen->classobj);
+ Py_VISIT(gen->exc_type);
+ Py_VISIT(gen->exc_value);
+ Py_VISIT(gen->exc_traceback);
+ return 0;
+}
+static void
+__Pyx_Generator_dealloc(PyObject *self)
+{
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject_GC_UnTrack(gen);
+ if (gen->gi_weakreflist != NULL)
+ PyObject_ClearWeakRefs(self);
+ PyObject_GC_Track(self);
+ if (gen->resume_label > 0) {
+ Py_TYPE(gen)->tp_del(self);
+ if (self->ob_refcnt > 0)
+ return; /* resurrected. :( */
+ }
+ PyObject_GC_UnTrack(self);
+ Py_CLEAR(gen->closure);
+ Py_CLEAR(gen->classobj);
+ Py_CLEAR(gen->exc_type);
+ Py_CLEAR(gen->exc_value);
+ Py_CLEAR(gen->exc_traceback);
+ PyObject_GC_Del(gen);
+}
+static void
+__Pyx_Generator_del(PyObject *self)
+{
+ PyObject *res;
+ PyObject *error_type, *error_value, *error_traceback;
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ if (gen->resume_label <= 0)
+ return ;
+ assert(self->ob_refcnt == 0);
+ self->ob_refcnt = 1;
+ __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
+ res = __Pyx_Generator_Close(self);
+ if (res == NULL)
+ PyErr_WriteUnraisable(self);
+ else
+ Py_DECREF(res);
+ __Pyx_ErrRestore(error_type, error_value, error_traceback);
+ /* Undo the temporary resurrection; can't use DECREF here, it would
+ * cause a recursive call.
+ */
+ assert(self->ob_refcnt > 0);
+ if (--self->ob_refcnt == 0)
+ return; /* this is the normal path out */
+ /* close() resurrected it! Make it look like the original Py_DECREF
+ * never happened.
+ */
+ {
+ Py_ssize_t refcnt = self->ob_refcnt;
+ _Py_NewReference(self);
+ self->ob_refcnt = refcnt;
+ }
+ assert(PyType_IS_GC(self->ob_type) &&
+ _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
+ /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
+ * we need to undo that. */
+ _Py_DEC_REFTOTAL;
+ /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
+ * chain, so no more to do there.
+ * If COUNT_ALLOCS, the original decref bumped tp_frees, and
+ * _Py_NewReference bumped tp_allocs: both of those need to be
+ * undone.
+ */
+#ifdef COUNT_ALLOCS
+ --self->ob_type->tp_frees;
+ --self->ob_type->tp_allocs;
+#endif
+}
+static PyMemberDef __pyx_Generator_memberlist[] = {
+ {(char *) "gi_running",
+ T_INT,
+ offsetof(__pyx_GeneratorObject, is_running),
+ READONLY,
+ NULL},
+ {0, 0, 0, 0, 0}
+};
+static PyMethodDef __pyx_Generator_methods[] = {
+ {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
+ {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
+ {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
+ {0, 0, 0, 0}
+};
+static PyTypeObject __pyx_GeneratorType = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("generator"), /*tp_name*/
+ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+#if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+#else
+ 0, /*reserved*/
+#endif
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ PyObject_GenericGetAttr, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
+ 0, /*tp_doc*/
+ (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
+ PyObject_SelfIter, /*tp_iter*/
+ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
+ __pyx_Generator_methods, /*tp_methods*/
+ __pyx_Generator_memberlist, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ 0, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ __Pyx_Generator_del, /*tp_del*/
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+#endif
+};
+static
+__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure)
+{
+ __pyx_GeneratorObject *gen =
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
+ if (gen == NULL)
+ return NULL;
+ gen->body = body;
+ gen->closure = closure;
+ Py_XINCREF(closure);
+ gen->is_running = 0;
+ gen->resume_label = 0;
+ gen->classobj = NULL;
+ gen->exc_type = NULL;
+ gen->exc_value = NULL;
+ gen->exc_traceback = NULL;
+ gen->gi_weakreflist = NULL;
+ PyObject_GC_Track(gen);
+ return gen;
+}
+static int __pyx_Generator_init(void)
+{
+ return PyType_Ready(&__pyx_GeneratorType);
+}
+
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+ int lineno, const char *filename) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
}
}
+static int __Pyx_check_binary_version(void) {
+ char ctversion[4], rtversion[4];
+ PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
+ PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
+ if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
+ char message[200];
+ PyOS_snprintf(message, sizeof(message),
+ "compiletime version %s of module '%.100s' "
+ "does not match runtime version %s",
+ ctversion, __Pyx_MODULE_NAME, rtversion);
+ #if PY_VERSION_HEX < 0x02050000
+ return PyErr_Warn(NULL, message);
+ #else
+ return PyErr_WarnEx(NULL, message, 1);
+ #endif
+ }
+ return 0;
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- long size, int strict)
+ size_t size, int strict)
{
PyObject *py_module = 0;
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
-
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(class_name);
- #else
- py_name = PyUnicode_FromString(class_name);
- #endif
+ py_name = __Pyx_PyIdentifier_FromString(class_name);
if (!py_name)
goto bad;
result = PyObject_GetAttr(py_module, py_name);
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
- if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
- PyErr_Warn(NULL, warning);
+ if (PyErr_Warn(NULL, warning) < 0) goto bad;
#else
- PyErr_WarnEx(NULL, warning, 0);
+ if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
bad:
Py_XDECREF(py_module);
Py_XDECREF(result);
- return 0;
+ return NULL;
}
#endif
static PyObject *__Pyx_ImportModule(const char *name) {
PyObject *py_name = 0;
PyObject *py_module = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(name);
- #else
- py_name = PyUnicode_FromString(name);
- #endif
+ py_name = __Pyx_PyIdentifier_FromString(name);
if (!py_name)
goto bad;
py_module = PyImport_Import(py_name);
}
#endif
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
}
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-
-static void __Pyx_AddTraceback(const char *funcname) {
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
- PyObject *py_globals = 0;
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
-
#if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(__pyx_filename);
+ py_srcfile = PyString_FromString(filename);
#else
- py_srcfile = PyUnicode_FromString(__pyx_filename);
+ py_srcfile = PyUnicode_FromString(filename);
#endif
if (!py_srcfile) goto bad;
- if (__pyx_clineno) {
+ if (c_line) {
#if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
#else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
#endif
}
else {
#endif
}
if (!py_funcname) goto bad;
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_code = PyCode_New(
+ py_code = __Pyx_PyCode_New(
0, /*int argcount,*/
- #if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
- #endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
- __pyx_lineno, /*int firstlineno,*/
+ py_line, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
- if (!py_code) goto bad;
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_globals = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = __pyx_lineno;
+ py_frame->f_lineno = py_line;
PyTraceBack_Here(py_frame);
bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
return 0;
}
+
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
projects / pysam.git / blobdiff