-/* Generated by Cython 0.14.1 on Fri Nov 25 19:51:23 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 PyBoolObject PyLongObject
#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_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_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
+ #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#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 "faidx.h"
#include "pysam_util.h"
#include "pythread.h"
+#ifdef _OPENMP
+#include <omp.h>
+#endif /* _OPENMP */
#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || defined(__INTEL_COMPILER)
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
#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 */
+/*--- 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.pyx":388
- * counter[0] += 1;
+/* "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;
-
-/* "csamtools.pyx":1537
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
* 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;
+};
-/* "csamtools.pyx":1717
- * 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;
};
-/* "csamtools.pyx":91
- * return dest
+/* "csamtools.pyx":518
+ * counter[0] += 1;
*
- * cdef class PileupRead # <<<<<<<<<<<<<<
- * cdef makePileupRead( bam_pileup1_t * src ):
- * '''fill a PileupRead object from a bam_pileup1_t * object.'''
+ * ctypedef struct MateData: # <<<<<<<<<<<<<<
+ * char * name
+ * bam1_t * mate
*/
+struct __pyx_t_9csamtools_MateData {
+ char *name;
+ bam1_t *mate;
+ uint32_t flag;
+};
-struct __pyx_obj_9csamtools_PileupRead {
+/* "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___pyx_scope_struct__genexpr {
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;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
-/* "csamtools.pxd":423
- * cdef char * _getrname( self, int tid )
+
+/* "csamtools.pxd":464
+ * cdef uint32_t _is_tail
*
* cdef class IteratorRow: # <<<<<<<<<<<<<<
* pass
*
*/
-
struct __pyx_obj_9csamtools_IteratorRow {
PyObject_HEAD
};
-/* "csamtools.pyx":1415
- * if self.owns_samfile: samclose( self.fp )
+
+/* "csamtools.pxd":487
+ * cdef int cnext(self)
*
* cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
- * """iterates over all mapped reads by chaining iterators over each reference
- * """
+ * cdef Samfile samfile
+ * cdef int tid
*/
-
struct __pyx_obj_9csamtools_IteratorRowAllRefs {
struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
struct __pyx_obj_9csamtools_Samfile *samfile;
struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
};
-/* "csamtools.pxd":426
- * pass
+
+/* "csamtools.pxd":480
+ * cdef int cnext(self)
*
* cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
* cdef bam1_t * b
* cdef samfile_t * fp
*/
-
struct __pyx_obj_9csamtools_IteratorRowAll {
struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
int owns_samfile;
};
-/* "csamtools.pyx":82
- * return dest
+
+/* "csamtools.pxd":449
+ * cdef char * _getrname( self, int tid )
*
- * cdef class PileupProxy # <<<<<<<<<<<<<<
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ * cdef class PileupProxy: # <<<<<<<<<<<<<<
+ * cdef bam_pileup1_t ** plp
+ * cdef int tid
*/
-
struct __pyx_obj_9csamtools_PileupProxy {
PyObject_HEAD
- bam_pileup1_t *plp;
+ bam_pileup1_t **plp;
int tid;
int pos;
int n_pu;
};
-/* "csamtools.pyx":1265
- * pass
+
+/* "csamtools.pxd":415
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length )
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
*
+ * # object that this AlignedRead represents
*/
-
-struct __pyx_obj_9csamtools_IteratorRowRegion {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
- bam1_t *b;
- int retval;
- struct __pyx_obj_9csamtools_Samfile *samfile;
- samfile_t *fp;
- int owns_samfile;
+struct __pyx_obj_9csamtools_AlignedRead {
+ PyObject_HEAD
+ bam1_t *_delegate;
};
-/* "csamtools.pyx":244
- * ## Public methods
- * ######################################################################
+
+/* "csamtools.pxd":408
+ * # Note: need to declare all C fields and methods here
+ * #
* cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
- *
+ * cdef char * _filename
+ * # pointer to fastafile
*/
-
struct __pyx_obj_9csamtools_Fastafile {
PyObject_HEAD
struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
faidx_t *fastafile;
};
-/* "csamtools.pyx":1461
- * raise StopIteration
+
+/* "csamtools.pxd":492
+ * cdef IteratorRowRegion rowiter
*
* cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile)*
- *
+ * 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;
int owns_samfile;
};
-/* "csamtools.pyx":1601
- * return ret
+
+/* "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;
int max_depth;
};
-/* "csamtools.pyx":1806
- * self.n_plp )
+
+/* "csamtools.pxd":536
+ * cdef int truncate
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
- * """iterates over all columns by chaining iterators over each reference
- * """
+ * pass
+ *
*/
-
struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "csamtools.pxd":394
+
+/* "csamtools.pxd":467
+ * pass
+ *
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * 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;
+ bam_iter_t iter;
+ bam1_t *b;
+ int retval;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ int owns_samfile;
+};
+
+
+/* "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+)" )
+ *
+ */
+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 *);
+};
+
+
+/* "csamtools.pxd":420
* cdef bam1_t * _delegate
*
* cdef class Samfile: # <<<<<<<<<<<<<<
* cdef char * _filename
* # pointer to samfile
*/
-
struct __pyx_obj_9csamtools_Samfile {
PyObject_HEAD
struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
int64_t start_offset;
};
-/* "csamtools.pyx":2902
+
+/* "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_SNPCall {
PyObject_HEAD
int _tid;
int _coverage;
};
-/* "csamtools.pyx":3456
- *
+
+/* "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;
};
-/* "csamtools.pyx":1777
- * self.iterdata.seq = NULL
+
+/* "csamtools.pxd":531
+ * cdef reset( self, tid, start, end )
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
+ * cdef int start
+ * cdef int end
*/
-
struct __pyx_obj_9csamtools_IteratorColumnRegion {
struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+ int start;
+ int end;
+ int truncate;
};
-/* "csamtools.pxd":389
- *
- * # need to declare all C fields and methods here
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+
+/* "csamtools.pxd":455
+ * cdef int n_pu
*
- * # object that this AlignedRead represents
+ * cdef class PileupRead: # <<<<<<<<<<<<<<
+ * cdef AlignedRead _alignment
+ * cdef int32_t _qpos
*/
-
-struct __pyx_obj_9csamtools_AlignedRead {
+struct __pyx_obj_9csamtools_PileupRead {
PyObject_HEAD
- bam1_t *_delegate;
+ 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;
};
-/* "csamtools.pyx":1601
+
+/* "csamtools.pyx":1766
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
-/* "csamtools.pyx":1777
+/* "csamtools.pyx":1931
* self.iterdata.seq = NULL
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
-/* "csamtools.pyx":1265
- * pass
+/* "csamtools.pyx":1461
+ *
*
* 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;
-/* "csamtools.pyx":1461
+/* "csamtools.pyx":1641
* raise StopIteration
*
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static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
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#define __Pyx_TraceDeclarations \
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#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
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#define __Pyx_TraceException() \
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#define __Pyx_TraceDeclarations
#define __Pyx_TraceCall(funcname, srcfile, firstlineno)
#define __Pyx_TraceException()
#define __Pyx_TraceReturn(result)
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#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*/
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+#include <string.h>
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static CYTHON_INLINE PyObject* __Pyx_tp_new(PyObject* type_obj) {
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-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*/
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-
-static void __Pyx_RaiseDoubleKeywordsError(
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+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
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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*/
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static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
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static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
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#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
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- else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
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- else {
- r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
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#define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_DelItemInt_Fast(o, i) : \
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static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
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+#define __Pyx_CyFunction_USED 1
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static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
-static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
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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*/
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+#define __Pyx_Generator_USED
+#include <structmember.h>
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+ PyObject *exc_type;
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+ PyObject *gi_weakreflist;
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+static int __pyx_Generator_init(void);
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+static void __Pyx_WriteUnraisable(const char *name, int clineno,
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+
+static int __Pyx_check_binary_version(void);
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+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
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+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
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+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
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-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+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 __builtin__ */
+/* Module declarations from 'cpython.float' */
-/* Module declarations from cpython.complex */
+/* Module declarations from '__builtin__' */
+/* Module declarations from 'cpython.complex' */
static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
-/* Module declarations from cpython.string */
-/* Module declarations from cpython.unicode */
+/* Module declarations from 'cpython.string' */
-/* Module declarations from cpython.dict */
+/* Module declarations from 'cpython.unicode' */
-/* Module declarations from cpython.instance */
+/* Module declarations from 'cpython.dict' */
-/* Module declarations from cpython.function */
+/* Module declarations from 'cpython.instance' */
-/* Module declarations from cpython.method */
+/* Module declarations from 'cpython.function' */
-/* Module declarations from cpython.weakref */
+/* Module declarations from 'cpython.method' */
-/* Module declarations from cpython.getargs */
+/* Module declarations from 'cpython.weakref' */
-/* Module declarations from cpython.pythread */
+/* Module declarations from 'cpython.getargs' */
-/* Module declarations from cpython.cobject */
+/* Module declarations from 'cpython.pythread' */
-/* Module declarations from cpython.oldbuffer */
+/* Module declarations from 'cpython.pystate' */
-/* Module declarations from cpython.set */
+/* Module declarations from 'cpython.cobject' */
-/* Module declarations from cpython.buffer */
+/* Module declarations from 'cpython.oldbuffer' */
-/* Module declarations from cpython.bytes */
+/* Module declarations from 'cpython.set' */
-/* Module declarations from cpython.pycapsule */
+/* Module declarations from 'cpython.buffer' */
-/* Module declarations from cpython */
+/* Module declarations from 'cpython.bytes' */
-/* Module declarations from csamtools */
+/* Module declarations from 'cpython.pycapsule' */
-static PyTypeObject *__pyx_ptype_9csamtools_file = 0;
+/* 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_IteratorRow = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 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_IteratorRowAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 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_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*/
static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
#define __Pyx_MODULE_NAME "csamtools"
-static int __pyx_module_is_main_csamtools = 0;
+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_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 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_5[] = "could not open file `%s`";
-static char __pyx_k_6[] = "I/O operation on closed file";
-static char __pyx_k_9[] = "no sequence/region supplied.";
-static char __pyx_k_11[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_12[] = "";
-static char __pyx_k_13[] = "start out of range (%i)";
-static char __pyx_k_14[] = "end out of range (%i)";
-static char __pyx_k_15[] = "%s:%i-%i";
-static char __pyx_k_17[] = "invalid file opening mode `%s`";
-static char __pyx_k_18[] = "-";
-static char __pyx_k_19[] = "http:";
-static char __pyx_k_20[] = "ftp:";
-static char __pyx_k_21[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
-static char __pyx_k_22[] = "unequal names and lengths of reference sequences";
-static char __pyx_k_23[] = "@SQ\tSN:%s\tLN:%s\n";
-static char __pyx_k_24[] = "file `%s` not found";
-static char __pyx_k_25[] = "could not open file (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_26[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_27[] = ".bai";
-static char __pyx_k_28[] = "error while opening index `%s` ";
-static char __pyx_k_31[] = "tid %i out of range 0<=tid<%i";
-static char __pyx_k_33[] = "[:-]";
-static char __pyx_k_35[] = "invalid reference `%s`";
-static char __pyx_k_36[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_38[] = "seek only available in bam files";
-static char __pyx_k_40[] = "seek no available in streams";
-static char __pyx_k_46[] = "fetch called on bamfile without index";
-static char __pyx_k_48[] = "callback functionality requires a region/reference";
-static char __pyx_k_50[] = "no index available for fetch";
-static char __pyx_k_52[] = "fetching by region is not available for sam files";
-static char __pyx_k_54[] = "fetch called for samfile without header";
-static char __pyx_k_56[] = "callback not implemented yet";
-static char __pyx_k_58[] = "read %s: is unpaired";
-static char __pyx_k_59[] = "mate %s: is unmapped";
-static char __pyx_k_60[] = "mate not found";
-static char __pyx_k_65[] = "counting functionality requires a region/reference";
-static char __pyx_k_68[] = "count for a region is not available for sam files";
-static char __pyx_k_71[] = "no index available for pileup";
-static char __pyx_k_74[] = "pileup of samfiles not implemented yet";
-static char __pyx_k_81[] = "Samfile.mapped only available in bam files";
-static char __pyx_k_84[] = "Samfile.unmapped only available in bam files";
-static char __pyx_k_89[] = "@";
-static char __pyx_k_91[] = "header line without '@': '%s'";
-static char __pyx_k_93[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_94[] = ":";
-static char __pyx_k_96[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_97[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_98[] = "@%s";
-static char __pyx_k_99[] = "%s:%s";
+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[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_101[] = "incomplete sequence information in '%s'";
-static char __pyx_k_103[] = "can not iterate over samfile without header";
-static char __pyx_k_106[] = "no index available for iteration";
-static char __pyx_k_112[] = "can only use this iterator on bam files";
-static char __pyx_k_113[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_114[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_116[] = "error during iteration";
-static char __pyx_k_119[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_120[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_121[] = "%c";
-static char __pyx_k_122[] = "create_string_buffer";
-static char __pyx_k_123[] = "<cccf";
-static char __pyx_k_124[] = "<cccb";
-static char __pyx_k_125[] = "<ccch";
-static char __pyx_k_126[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_127[] = "<ccci";
-static char __pyx_k_128[] = "<cccB";
-static char __pyx_k_129[] = "<cccH";
-static char __pyx_k_130[] = "<cccI";
-static char __pyx_k_131[] = "<cccc";
-static char __pyx_k_132[] = "<ccc%is";
-static char __pyx_k_133[] = "tags field too large";
-static char __pyx_k_135[] = "tag '%s' not present";
-static char __pyx_k_136[] = "Contig index";
-static char __pyx_k_137[] = "Mapped position on contig";
-static char __pyx_k_138[] = "Contig index for mate pair";
-static char __pyx_k_139[] = "Position of mate pair";
-static char __pyx_k_140[] = "Insert size";
-static char __pyx_k_141[] = "Binary flag";
-static char __pyx_k_142[] = "Count of cigar entries";
-static char __pyx_k_143[] = "Cigar entries";
-static char __pyx_k_144[] = "Mapping quality";
-static char __pyx_k_145[] = "Bam index bin number";
-static char __pyx_k_146[] = "Length of query name";
-static char __pyx_k_147[] = "Query name";
-static char __pyx_k_148[] = "Length of query sequence";
-static char __pyx_k_149[] = "Query sequence";
-static char __pyx_k_150[] = "Quality scores";
-static char __pyx_k_151[] = "Length of auxilary data";
-static char __pyx_k_152[] = "Maximum data length";
-static char __pyx_k_153[] = "Current data length";
-static char __pyx_k_154[] = "%-30s %-10s= %s";
-static char __pyx_k_155[] = "(";
-static char __pyx_k_156[] = ")";
-static char __pyx_k_157[] = "This class cannot be instantiated from Python";
-static char __pyx_k_162[] = "No such file or directory: '%s'";
-static char __pyx_k_163[] = "-o";
-static char __pyx_k_164[] = "option -o is forbidden in samtools view";
-static char __pyx_k_166[] = "_rms_mapping_quality";
-static char __pyx_k_167[] = "can only IndexReads on bam files";
-static char __pyx_k_168[] = "read %s not found";
-static char __pyx_k_169[] = "the query name (None if not present)";
-static char __pyx_k_170[] = "the :term:`cigar` alignment (None if not present).\n ";
-static char __pyx_k_171[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_172[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_173[] = "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_174[] = "aligned query sequence quality values (None if not present)";
-static char __pyx_k_175[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_176[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_177[] = "Length of the aligned query sequence";
-static char __pyx_k_178[] = "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_179[] = "properties flag";
-static char __pyx_k_180[] = "\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_181[] = "\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_182[] = "0-based leftmost coordinate";
-static char __pyx_k_183[] = "properties bin";
-static char __pyx_k_184[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_185[] = "aligned end position of the read on the reference genome. Returns\n None if not available.";
-static char __pyx_k_186[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
-static char __pyx_k_187[] = "mapping quality";
-static char __pyx_k_188[] = "the :term:`reference` id of the mate \n deprecated, use RNEXT instead.\n ";
-static char __pyx_k_189[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_190[] = "the position of the mate\n deprecated, use PNEXT instead.";
-static char __pyx_k_191[] = "the position of the mate";
-static char __pyx_k_192[] = "the insert size\n deprecated: use tlen instead";
-static char __pyx_k_193[] = "the insert size";
-static char __pyx_k_194[] = "true if read is paired in sequencing";
-static char __pyx_k_195[] = "true if read is mapped in a proper pair";
-static char __pyx_k_196[] = "true if read itself is unmapped";
-static char __pyx_k_197[] = "true if the mate is unmapped";
-static char __pyx_k_198[] = "true if read is mapped to reverse strand";
-static char __pyx_k_199[] = "true is read is mapped to reverse strand";
-static char __pyx_k_200[] = "true if this is read1";
-static char __pyx_k_201[] = "true if this is read2";
-static char __pyx_k_202[] = "true if not primary alignment";
-static char __pyx_k_203[] = "true if QC failure";
-static char __pyx_k_204[] = "true if optical or PCR duplicate";
-static char __pyx_k_205[] = "a list of reference positions that this read aligns to.";
-static char __pyx_k_206[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_207[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_208[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_209[] = "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_210[] = "total number of mapped reads in file.\n ";
-static char __pyx_k_211[] = "total number of unmapped reads in file.\n ";
-static char __pyx_k_212[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_213[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
-static char __pyx_k_214[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_215[] = "number of reads mapping to this column.";
-static char __pyx_k_216[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_217[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_218[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_219[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_220[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_221[] = "current sequence length.";
-static char __pyx_k_222[] = "nucleotide position of SNP.";
-static char __pyx_k_223[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_224[] = "the genotype called.";
-static char __pyx_k_225[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_226[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_227[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_228[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_229[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_230[] = "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_231[] = "\n stderr is captured. \n ";
-static char __pyx_k_232[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_238[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+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__UR[] = "UR";
static char __pyx_k__VN[] = "VN";
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__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__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__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__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__text[] = "text";
static char __pyx_k__view[] = "view";
+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__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
-static char __pyx_k__cnext[] = "cnext";
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_plp[] = "n_plp";
static char __pyx_k__qname[] = "qname";
static char __pyx_k__rname[] = "rname";
static char __pyx_k__setfd[] = "setfd";
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__append[] = "append";
static char __pyx_k__ctypes[] = "ctypes";
+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__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__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____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__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__pileups[] = "pileups";
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____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__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__isremote[] = "isremote";
-static char __pyx_k__isstream[] = "isstream";
-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__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__fastafile[] = "fastafile";
static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__max_depth[] = "max_depth";
-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__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__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__nreferences[] = "nreferences";
-static char __pyx_k__pileup_iter[] = "pileup_iter";
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__catch_stderr[] = "catch_stderr";
static char __pyx_k__catch_stdout[] = "catch_stdout";
-static char __pyx_k__owns_samfile[] = "owns_samfile";
-static char __pyx_k__start_offset[] = "start_offset";
+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__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__mapping_quality[] = "mapping_quality";
static char __pyx_k____getattribute__[] = "__getattribute__";
static char __pyx_k__referencelengths[] = "referencelengths";
static char __pyx_k__consensus_quality[] = "consensus_quality";
-static char __pyx_k__setupIteratorData[] = "setupIteratorData";
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_103;
-static PyObject *__pyx_kp_s_106;
-static PyObject *__pyx_kp_s_11;
-static PyObject *__pyx_kp_s_112;
+static PyObject *__pyx_kp_s_102;
+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_110;
+static PyObject *__pyx_kp_s_111;
static PyObject *__pyx_kp_s_113;
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-static PyObject *__pyx_n_s_122;
-static PyObject *__pyx_kp_s_123;
-static PyObject *__pyx_kp_s_124;
+static PyObject *__pyx_kp_s_119;
static PyObject *__pyx_kp_s_125;
static PyObject *__pyx_kp_s_126;
static PyObject *__pyx_kp_s_127;
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static PyObject *__pyx_kp_s_145;
-static PyObject *__pyx_kp_s_146;
-static PyObject *__pyx_kp_s_147;
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static PyObject *__pyx_kp_s_148;
static PyObject *__pyx_kp_s_149;
static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_155;
static PyObject *__pyx_kp_s_156;
static PyObject *__pyx_kp_s_157;
+static PyObject *__pyx_kp_s_158;
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static PyObject *__pyx_kp_s_162;
static PyObject *__pyx_kp_s_163;
static PyObject *__pyx_kp_s_164;
-static PyObject *__pyx_n_s_166;
+static PyObject *__pyx_kp_s_165;
+static PyObject *__pyx_kp_s_166;
static PyObject *__pyx_kp_s_167;
static PyObject *__pyx_kp_s_168;
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static PyObject *__pyx_kp_s_17;
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static PyObject *__pyx_kp_s_24;
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static PyObject *__pyx_kp_s_31;
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static PyObject *__pyx_kp_s_33;
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static PyObject *__pyx_kp_s_35;
static PyObject *__pyx_kp_s_36;
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static PyObject *__pyx_kp_s_38;
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static PyObject *__pyx_kp_s_46;
static PyObject *__pyx_kp_s_48;
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static PyObject *__pyx_kp_s_60;
-static PyObject *__pyx_kp_s_65;
-static PyObject *__pyx_kp_s_68;
+static PyObject *__pyx_kp_s_62;
+static PyObject *__pyx_kp_s_64;
+static PyObject *__pyx_kp_s_66;
+static PyObject *__pyx_kp_s_69;
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static PyObject *__pyx_kp_s_71;
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-static PyObject *__pyx_kp_s_81;
-static PyObject *__pyx_kp_s_84;
-static PyObject *__pyx_kp_s_89;
+static PyObject *__pyx_kp_s_76;
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+static PyObject *__pyx_kp_s_85;
static PyObject *__pyx_kp_s_9;
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-static PyObject *__pyx_kp_s_93;
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-static PyObject *__pyx_kp_s_97;
-static PyObject *__pyx_kp_s_98;
-static PyObject *__pyx_kp_s_99;
+static PyObject *__pyx_kp_s_92;
+static PyObject *__pyx_kp_s_95;
+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__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__IteratorRow;
+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__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____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___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___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__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__append;
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__c;
static PyObject *__pyx_n_s__calcsize;
static PyObject *__pyx_n_s__callback;
-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__collections;
+static PyObject *__pyx_n_s__compile;
static PyObject *__pyx_n_s__consensus_quality;
-static PyObject *__pyx_n_s__core;
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__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__fastafile;
static PyObject *__pyx_n_s__fd;
static PyObject *__pyx_n_s__fields;
static PyObject *__pyx_n_s__filename;
static PyObject *__pyx_n_s__fileno;
+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__getdefaultencoding;
static PyObject *__pyx_n_s__gettid;
-static PyObject *__pyx_n_s__hash;
+static PyObject *__pyx_n_s__h;
static PyObject *__pyx_n_s__header;
static PyObject *__pyx_n_s__i;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__indel;
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__isstream;
+static PyObject *__pyx_n_s__islower;
static PyObject *__pyx_n_s__isupper;
-static PyObject *__pyx_n_s__iter;
-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;
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_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__ord;
static PyObject *__pyx_n_s__os;
-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_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__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__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__record;
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__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__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__start_offset;
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__tempfile;
static PyObject *__pyx_n_s__template;
static PyObject *__pyx_n_s__text;
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_16;
static PyObject *__pyx_int_536870912;
static PyObject *__pyx_int_4294967295;
static PyObject *__pyx_int_neg_2147483648;
-static PyObject *__pyx_k_16;
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-static PyObject *__pyx_k_62;
-static int __pyx_k_115;
-static PyObject *__pyx_k_160;
-static PyObject *__pyx_k_161;
+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_7;
static PyObject *__pyx_k_tuple_8;
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-static PyObject *__pyx_k_tuple_32;
-static PyObject *__pyx_k_tuple_34;
-static PyObject *__pyx_k_tuple_37;
+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_41;
+static PyObject *__pyx_k_tuple_40;
static PyObject *__pyx_k_tuple_42;
-static PyObject *__pyx_k_tuple_43;
-static PyObject *__pyx_k_tuple_45;
+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_64;
-static PyObject *__pyx_k_tuple_66;
+static PyObject *__pyx_k_tuple_65;
static PyObject *__pyx_k_tuple_67;
-static PyObject *__pyx_k_tuple_69;
-static PyObject *__pyx_k_tuple_70;
+static PyObject *__pyx_k_tuple_68;
static PyObject *__pyx_k_tuple_72;
-static PyObject *__pyx_k_tuple_73;
+static PyObject *__pyx_k_tuple_74;
static PyObject *__pyx_k_tuple_75;
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static PyObject *__pyx_k_tuple_77;
static PyObject *__pyx_k_tuple_78;
-static PyObject *__pyx_k_tuple_79;
static PyObject *__pyx_k_tuple_80;
-static PyObject *__pyx_k_tuple_82;
+static PyObject *__pyx_k_tuple_81;
static PyObject *__pyx_k_tuple_83;
-static PyObject *__pyx_k_tuple_85;
+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_92;
-static PyObject *__pyx_k_tuple_95;
-static PyObject *__pyx_k_tuple_102;
-static PyObject *__pyx_k_tuple_104;
-static PyObject *__pyx_k_tuple_105;
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-static PyObject *__pyx_k_tuple_109;
-static PyObject *__pyx_k_tuple_110;
-static PyObject *__pyx_k_tuple_111;
+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;
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-static PyObject *__pyx_k_tuple_237;
-
-/* "csamtools.pyx":76
- * #####################################################################
- * cdef class AlignedRead
- * cdef makeAlignedRead(bam1_t * src): # <<<<<<<<<<<<<<
- * '''enter src into AlignedRead.'''
- * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
- */
-
-static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
- struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
+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;
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else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
+ 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_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
+ 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_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
+ 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_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
+ 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_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o);
+ 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_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
+ 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_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o);
+ return __pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
+ 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_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o);
+ 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_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
+ 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_pf_9csamtools_11AlignedRead_9is_paired_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
+ 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_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
+ 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_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
+ 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_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
+ 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_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
+ 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_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
+ 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_pf_9csamtools_11AlignedRead_8is_read1_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
+ 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_pf_9csamtools_11AlignedRead_8is_read2_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
+ 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_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
+ 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_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
+ 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_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(o, v);
+ return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
+ 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_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)},
+ {__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[] = {
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- {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_171), 0},
- {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_172), 0},
- {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_173), 0},
- {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_174), 0},
- {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_175), 0},
- {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_176), 0},
- {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_177), 0},
- {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_178), 0},
- {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_179), 0},
- {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_180), 0},
- {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_181), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_182), 0},
- {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_183), 0},
- {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_184), 0},
- {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_185), 0},
- {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_186), 0},
- {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_187), 0},
- {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_188), 0},
- {(char *)"rnext", __pyx_getprop_9csamtools_11AlignedRead_rnext, __pyx_setprop_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_189), 0},
- {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_190), 0},
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- {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_192), 0},
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- {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
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+ {(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},
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+ {(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},
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+ {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
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+ {(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},
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+ {(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}
};
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&__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
&__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/
+ __pyx_pw_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_11AlignedRead_2__str__, /*tp_str*/
+ __pyx_pw_9csamtools_11AlignedRead_5__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_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 "), /*tp_doc*/
+ __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_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
+ __pyx_pw_9csamtools_11AlignedRead_1__init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
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) {
+ if (__pyx_pw_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_7Samfile_15__dealloc__(o);
+ __pyx_pw_9csamtools_7Samfile_31__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
+ return __pyx_pw_9csamtools_7Samfile_8filename_1__get__(o);
+}
+
+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_7Samfile_references(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_7Samfile_10references_1__get__(o);
+}
+
+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 PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_11nreferences___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_Samfile[] = {
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+ {(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_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
+};
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+ 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*/
+};
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+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
+};
+
+static 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_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_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_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_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ return o;
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
+static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_7lengths___get__(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_7Samfile_mapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
+ return __pyx_pw_9csamtools_11PileupProxy_1n_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_8unmapped___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_7Samfile_text(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
+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_7Samfile_header(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_6header___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_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)},
- {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)},
+static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
- {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_207), 0},
- {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_208), 0},
- {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_209), 0},
- {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_210), 0},
- {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_211), 0},
- {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_212), 0},
- {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_213), 0},
+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_Samfile = {
+static PyNumberMethods __pyx_tp_as_number_PileupProxy = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Samfile = {
+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_Samfile = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupProxy = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_Samfile = {
+static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Samfile, /*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_Samfile, /*tp_as_number*/
- &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Samfile, /*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_Samfile, /*tp_as_buffer*/
+ &__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("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,\n add_sq_text = False )*\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.\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 "), /*tp_doc*/
+ __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*/
- __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_Samfile, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_Samfile, /*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_Samfile, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *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_PileupRead *)o);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
+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 PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
+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_IteratorRow = {
+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_IteratorRow = {
+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_IteratorRow = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
+static PyTypeObject __pyx_type_9csamtools_PileupRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRow, /*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_IteratorRow, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRow, /*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_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*/
+ &__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*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
+ __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_IteratorRow, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-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);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
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;
- }
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_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRow = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
+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_IteratorRowAll = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*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_IteratorRowAll, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAll, /*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*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
+ &__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("*(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*/
+ __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*/
- __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAll, /*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_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- 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_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_PileupProxy(PyObject *o) {
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_1n___get__(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_pw_9csamtools_17IteratorRowRegion_7__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);
}
-static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
+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;
}
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ return 0;
}
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
+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 PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
+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 struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_214), 0},
- {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_215), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
- {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_216), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_PileupProxy = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = {
+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_PileupProxy = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_PileupProxy, /*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_PileupProxy, /*tp_as_number*/
- &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_PileupProxy, /*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*/
- __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__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*/
+ &__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_PileupProxy, /*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*/
- __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
+ 0, /*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_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_PileupProxy, /*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_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-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);
+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_PileupRead *)o);
- p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ 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 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;
+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);
}
- 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_pf_9csamtools_10PileupRead_9alignment___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
+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 struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
- {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_217), 0},
- {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_218), 0},
- {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_219), 0},
- {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_220), 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 = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_PileupRead = {
+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_PileupRead = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_PileupRead = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_PileupRead, /*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_PileupRead, /*tp_as_number*/
- &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_PileupRead, /*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*/
- __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__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*/
+ &__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*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_PileupRead, /*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*/
- __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
+ 0, /*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_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_PileupRead, /*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_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);
+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_Fastafile *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
- if (__pyx_pf_9csamtools_9Fastafile___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 void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
+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;
}
- (*Py_TYPE(o)->tp_free)(o);
+ 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 PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
+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_Fastafile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)},
+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 struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Fastafile = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
+ 0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
+ 0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_Fastafile = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Fastafile, /*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_Fastafile, /*tp_as_number*/
- &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Fastafile, /*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_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*/
+ &__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_Fastafile, /*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*/
- __pyx_getsets_9csamtools_Fastafile, /*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_Fastafile, /*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_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p;
+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_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) {
+ 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_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)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_17IteratorRowRegion_3__dealloc__(o);
+ __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(p->positions);
__pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
+ 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->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ if (p->positions) {
+ e = (*v)(p->positions, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)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->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ tmp = ((PyObject*)p->positions);
+ p->positions = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)},
+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 PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
+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_IteratorRowRegion = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*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_IteratorRowRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowRegion, /*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*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
+ &__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, 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*/
+ __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*/
- __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowRegion, /*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*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowRegion, /*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_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+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_IteratorRowAllRefs *)o);
+ 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->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
+ 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_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)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_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->rowiter));
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+ Py_XDECREF(((PyObject *)p->fastafile));
+ Py_XDECREF(p->stepper);
+ (*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(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_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;
+ 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->rowiter) {
- e = (*v)(((PyObject*)p->rowiter), 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_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
+ 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->rowiter);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ 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_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
+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_IteratorRowAllRefs = {
+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_IteratorRowAllRefs = {
+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_IteratorRowAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*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_IteratorRowAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAllRefs, /*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_IteratorRowAllRefs, /*tp_as_buffer*/
+ &__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("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*/
+ __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*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
+ __pyx_pw_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __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_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_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;
- }
- 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_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- 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;
- }
- if (p->positions) {
- e = (*v)(p->positions, a); if (e) return e;
- }
- return 0;
-}
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools_IteratorColumn, /*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_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-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_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;
+ 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;
}
- tmp = ((PyObject*)p->positions);
- p->positions = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+ return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)},
+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_IteratorRowSelection = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
+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_IteratorRowSelection = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*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_IteratorRowSelection, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowSelection, /*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_IteratorRowSelection, /*tp_as_buffer*/
+ &__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("*(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_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*/
- __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
+ 0, /*tp_iter*/
+ __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_IteratorRowSelection, /*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_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-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);
+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;
- 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_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 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_14IteratorColumn_4__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 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_14IteratorColumn_seq_len(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
+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 struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_221), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
+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_IteratorColumn = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
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_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_IteratorColumn, /*tp_as_buffer*/
+ &__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("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 max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/
+ __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_14IteratorColumn_1__iter__, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
+ 0, /*tp_iter*/
+ __pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_IteratorColumn, /*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_IteratorColumn, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*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_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IndexedReads *p;
+ 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;
- }
+ p = ((struct __pyx_obj_9csamtools_IndexedReads *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->index = Py_None; Py_INCREF(Py_None);
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)},
+static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(p->index);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->index) {
+ e = (*v)(p->index, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->index);
+ p->index = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
+ {__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}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
+static PyNumberMethods __pyx_tp_as_number_IndexedReads = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
+static PySequenceMethods __pyx_tp_as_sequence_IndexedReads = {
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_IndexedReads = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
+static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
+static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IndexedReads, /*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_IndexedReads, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IndexedReads, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IndexedReads, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IndexedReads, /*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*/
+ __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_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_IndexedReads, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pw_9csamtools_12IndexedReads_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_IndexedReads, /*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_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
+ 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;
- }
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)},
+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}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
+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}
+};
+
+static PyNumberMethods __pyx_tp_as_number_SNPCall = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
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_SNPCall = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_SNPCall = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_SNPCall, /*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_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*/
- 0, /*tp_str*/
+ __pyx_pw_9csamtools_7SNPCall_1__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_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*/
+ &__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*/
- __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_9csamtools_SNPCall, /*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_IteratorColumnAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_SNPCall, /*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___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_SNPCall(PyObject *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 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 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 PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
+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_SNPCall[] = {
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct__genexpr[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_214), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_222), 0},
- {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_223), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_224), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_SNPCall = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__genexpr = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__genexpr = {
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___pyx_scope_struct__genexpr = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_SNPCall = {
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
+ __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_SNPCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr, /*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___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*/
- __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_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__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_SNPCall, /*tp_methods*/
+ __pyx_methods_9csamtools___pyx_scope_struct__genexpr, /*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___pyx_scope_struct__genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IndexedReads *p;
+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_IndexedReads *)o);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->index = Py_None; Py_INCREF(Py_None);
+ 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_IndexedReads(PyObject *o) {
- struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
- {
- PyObject *etype, *eval, *etb;
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- __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o);
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- PyErr_Restore(etype, eval, etb);
- }
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(p->index);
+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_IndexedReads(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return 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->index) {
- e = (*v)(p->index, 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_IndexedReads(PyObject *o) {
- struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
+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->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ tmp = ((PyObject*)p->__pyx_v_x);
+ p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
- tmp = ((PyObject*)p->index);
- p->index = Py_None; Py_INCREF(Py_None);
+ 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;
}
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- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)},
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndexedReads = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndexedReads = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndexedReads = {
+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_IndexedReads = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
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__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 = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1265; __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_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
+ __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 = 1265; __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 = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1415; __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_3__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
+ __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 = 1415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1461; __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_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
+ __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 = 1461; __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 = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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.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 = 1601; __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 = 1601; __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 = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1777; __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_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
+ __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 = 1777; __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 = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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 = 1806; __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_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
+ __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 = 1806; __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 = 1806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2902; __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 = 2902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
- if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3456; __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 = 3456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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;}
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__Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorRow));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorRow));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorColumn));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorColumn));
__Pyx_INCREF(((PyObject *)__pyx_n_s__AlignedRead));
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__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));
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__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));
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__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));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupRead));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IndexedReads));
- PyList_SET_ITEM(__pyx_t_3, 8, ((PyObject *)__pyx_n_s__IndexedReads));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndexedReads));
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- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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- 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;
-
- /* "cpython/type.pxd":2
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- * cdef extern from "Python.h": # <<<<<<<<<<<<<<
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+ __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");
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Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
PyErr_SetString(PyExc_ImportError, "init csamtools");
}
/* Runtime support code */
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+static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
+ PyObject *m = NULL, *p = NULL;
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+ if (!m) goto end;
+ p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
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+ r = PyLong_AsVoidPtr(p);
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+ Py_XDECREF(p);
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+}
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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;
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-
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:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
-
return py_code;
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#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_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");
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-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "too many values to unpack (expected %d)", (int)expected);
- #else
- "too many values to unpack (expected %zd)", expected);
- #endif
-}
-
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
- PyObject *item;
- if (!(item = PyIter_Next(iter))) {
- if (!PyErr_Occurred()) {
- __Pyx_RaiseNeedMoreValuesError(index);
- }
- }
- return item;
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-
-static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
- PyObject *item;
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- __Pyx_RaiseTooManyValuesError(expected);
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- return -1;
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-
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
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-{
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- while (PyDict_Next(kwdict, &pos, &key, 0)) {
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- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
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- goto invalid_keyword_type;
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- if ((!kw_allowed) && unlikely(key))
- goto invalid_keyword;
- return 1;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- return 0;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
- 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;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_Restore(type, value, tb);
+#endif
}
-
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
}
-
#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
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;
"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 (!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
}
#endif
}
-
__Pyx_ErrRestore(type, value, tb);
return;
raise_error:
Py_XDECREF(tb);
return;
}
-
#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
}
if (value == Py_None)
value = 0;
-
if (PyExceptionInstance_Check(type)) {
if (value) {
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;
Py_XDECREF(tmp_tb);
}
}
-
-bad:
- return;
+bad:
+ return;
+}
+#endif
+
+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 int __Pyx_CheckKeywordStrings(
+ PyObject *kwdict,
+ const char* function_name,
+ int kw_allowed)
+{
+ PyObject* key = 0;
+ Py_ssize_t pos = 0;
+ while (PyDict_Next(kwdict, &pos, &key, 0)) {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
+ #else
+ if (unlikely(!PyUnicode_Check(key)))
+ #endif
+ goto invalid_keyword_type;
+ }
+ if ((!kw_allowed) && unlikely(key))
+ goto invalid_keyword;
+ return 1;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ return 0;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+ return 0;
}
-#endif
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name,
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
Py_ssize_t num_found)
{
Py_ssize_t num_expected;
- const char *number, *more_or_less;
-
+ const char *more_or_less;
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
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);
+ "%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,
+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) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
}
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) {
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
PyObject *py_import = 0;
PyObject *empty_list = 0;
PyObject *module = 0;
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,
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+ 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);
#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, "__class__");
+ metaclass = PyObject_GetAttrString(base, (char *)"__class__");
if (!metaclass) {
PyErr_Clear();
metaclass = (PyObject*) Py_TYPE(base);
PyObject *modname) {
PyObject *result;
PyObject *metaclass;
-
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
-
/* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
return result;
}
-
-static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
- __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
+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->func.m_ml = ml;
- Py_XINCREF(self);
- op->func.m_self = self;
- Py_XINCREF(module);
- op->func.m_module = module;
- PyObject_GC_Track(op);
- return (PyObject *)op;
-}
-
-static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
- PyObject_GC_UnTrack(m);
- Py_XDECREF(m->func.m_self);
- Py_XDECREF(m->func.m_module);
+ 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 PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
- if (obj == Py_None)
- obj = NULL;
- return PyMethod_New(func, obj, type);
+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 int __pyx_binding_PyCFunctionType_init(void) {
- __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
- __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
- __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
- __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
- if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
- return -1;
+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);
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+}
+
+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);
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+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
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+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
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+ little, !is_unsigned);
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+}
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint16_t(uint16_t val) {
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+ 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);
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+ 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;
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+ little, !is_unsigned);
+ }
+}
+
+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);
}
- __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
- return 0;
-
}
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);
}
}
}
}
-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_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;
} else {
int one = 1; int little = (int)*(unsigned char *)&one;
unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(int64_t),
+ return _PyLong_FromByteArray(bytes, sizeof(int64_t),
little, !is_unsigned);
}
}
}
}
+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(uint8_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint8_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint8_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint8_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint8_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint8_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint8_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint8_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint8_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint8_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint8_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint8_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint8_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint8_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint8_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 (uint8_t)-1;
+ }
+}
+
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
const int is_unsigned = const_zero < neg_one;
}
}
-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_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);
module_name, class_name);
goto bad;
}
- if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
+ 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) {
+ 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);
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