-/* Generated by Cython 0.14.1 on Fri Nov 25 20:32:50 2011 */
+/* Generated by Cython 0.17.1 on Tue Nov 20 16:47:00 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 )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#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 PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) PyInt_AsLong(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && !PyComplex_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"
+ #define CYTHON_FORMAT_SSIZE_T "z"
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
#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_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define __Pyx_PyUnicode_READY(op) (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]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#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_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
#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__ctabix
#define __PYX_HAVE_API__ctabix
#include "string.h"
#include "stdlib.h"
#include "bgzf.h"
#include "tabix.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 PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
+#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[] = {
"ctabix.pyx",
+ "TabProxies.pxd",
+ "type.pxd",
"bool.pxd",
"complex.pxd",
- "TabProxies.pxd",
};
-/* Type declarations */
-
-/* "ctabix.pxd":178
+/*--- Type declarations ---*/
+struct __pyx_obj_6ctabix_Parser;
+struct __pyx_obj_6ctabix_asVCF;
+struct __pyx_obj_10TabProxies_TupleProxy;
+struct __pyx_obj_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_10TabProxies_BedProxy;
+struct __pyx_obj_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_10TabProxies_VCFProxy;
+struct __pyx_obj_10TabProxies_GTFProxy;
+struct __pyx_obj_6ctabix_TabixIterator;
+struct __pyx_obj_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_6ctabix_Tabixfile;
+struct __pyx_obj_6ctabix_asGTF;
+struct __pyx_obj_6ctabix_asBed;
+struct __pyx_obj_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_6ctabix_asTuple;
+
+/* "ctabix.pxd":190
* cdef tabix_t * tabixfile
*
* cdef class Parser: # <<<<<<<<<<<<<<
* pass
+ *
*/
-
struct __pyx_obj_6ctabix_Parser {
PyObject_HEAD
};
-/* "ctabix.pyx":389
- * return r
+
+/* "ctabix.pxd":202
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class asVCF( Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a VCF record with
- * the following fields:
*/
-
struct __pyx_obj_6ctabix_asVCF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":42
+
+/* "TabProxies.pxd":41
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
*
* cdef:
*/
-
struct __pyx_obj_10TabProxies_TupleProxy {
PyObject_HEAD
struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
int is_modified;
};
-/* "TabProxies.pxd":78
- * cdef update( self, char * buffer, size_t nbytes )
+
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( self )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
* pass
*
*/
-
struct __pyx_obj_10TabProxies_NamedTupleProxy {
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "TabProxies.pxd":81
+
+/* "TabProxies.pxd":72
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-
struct __pyx_obj_10TabProxies_BedProxy {
struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
char *contig;
int bedfields;
};
-/* "TabProxies.pxd":92
+
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
+ *
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
+ */
+struct __pyx_obj_6ctabix_tabix_copy_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab;
+ FILE *infile;
+ struct __pyx_obj_6ctabix_Parser *parser;
+};
+
+
+/* "TabProxies.pxd":83
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-
struct __pyx_obj_10TabProxies_VCFProxy {
struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
char *contig;
uint32_t pos;
};
-/* "TabProxies.pxd":61
+
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-
struct __pyx_obj_10TabProxies_GTFProxy {
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
- char *contig;
- char *source;
- char *feature;
- uint32_t start;
- uint32_t end;
- char *score;
- char *strand;
- char *frame;
- char *attributes;
+ char *_attributes;
int hasOwnAttributes;
};
-/* "ctabix.pyx":193
- * if self._filename != NULL: free( self._filename )
+
+/* "ctabix.pxd":182
+ * cdef char * _filename
*
* cdef class TabixIterator: # <<<<<<<<<<<<<<
- * """iterates over rows in *tabixfile* in region
- * given by *tid*, *start* and *end*.
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-
struct __pyx_obj_6ctabix_TabixIterator {
PyObject_HEAD
ti_iter_t iterator;
tabix_t *tabixfile;
};
-/* "ctabix.pyx":428
- * #########################################################
- * #########################################################
- * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
- * """iterates over mapped reads in a region.
+
+/* "ctabix.pxd":205
+ * pass
*
+ * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-
struct __pyx_obj_6ctabix_TabixIteratorParsed {
PyObject_HEAD
ti_iter_t iterator;
struct __pyx_obj_6ctabix_Parser *parser;
};
-/* "ctabix.pyx":248
- * ti_iter_destroy(self.iterator)
+
+/* "ctabix.pxd":186
+ * cdef tabix_t * tabixfile
*
* cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * """return header lines.
- * """
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-
struct __pyx_obj_6ctabix_TabixHeaderIterator {
PyObject_HEAD
ti_iter_t iterator;
tabix_t *tabixfile;
};
+
/* "ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
*
+ * # pointer to tabixfile
*/
-
struct __pyx_obj_6ctabix_Tabixfile {
PyObject_HEAD
- char *_filename;
tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
};
-/* "ctabix.pyx":312
- * return r
+
+/* "ctabix.pxd":196
+ * pass
*
* cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a GTF record with the following
- * fields:
+ * pass
+ *
*/
-
struct __pyx_obj_6ctabix_asGTF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pyx":349
- * return r
+
+/* "ctabix.pxd":199
+ * pass
+ *
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class asBed( Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a bed record
- * with the following fields:
*/
-
struct __pyx_obj_6ctabix_asBed {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pyx":299
- * pass
+
+/* "ctabix.pxd":210
+ * cdef Parser parser
+ *
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
+ */
+struct __pyx_obj_6ctabix_tabix_inplace_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab;
+ FILE *infile;
+ char *buffer;
+ size_t size;
+ struct __pyx_obj_6ctabix_Parser *parser;
+};
+
+
+/* "ctabix.pxd":193
+ * pass
*
* cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a python tuple.
+ * pass
*
*/
-
struct __pyx_obj_6ctabix_asTuple {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":42
+
+/* "ctabix.pyx":768
+ * return self.__cnext__()
+ *
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
+ *
+ */
+
+struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *);
+};
+static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator;
+
+
+/* "TabProxies.pxd":41
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "TabProxies.pxd":78
- * cdef update( self, char * buffer, size_t nbytes )
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( self )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
* pass
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pxd":92
+/* "TabProxies.pxd":83
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "TabProxies.pxd":81
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+ char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *);
+};
+static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+
+
+/* "TabProxies.pxd":72
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
-/* "TabProxies.pxd":61
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+/* "ctabix.pyx":706
+ * ## Iterators for parsing through unindexed files.
+ * #########################################################
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
*
- * cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_GTFProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *);
};
-static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
-
+static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator;
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+ #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0)
+ #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
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#define __Pyx_GOTREF(r)
#define __Pyx_GIVEREF(r)
+ #define __Pyx_XINCREF(r) Py_XINCREF(r)
#define __Pyx_XDECREF(r) Py_XDECREF(r)
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-#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0)
-#define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r);} } while(0)
+#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
+#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
- const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name, PyObject* kw_name); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
+
+#include <string.h>
+
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
+
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
Py_DECREF(j);
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-
#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
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- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
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- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
-
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
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static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
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- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
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+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
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+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
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-
-
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
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-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
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- else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
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}
- else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
- r = PySequence_GetItem(o, i);
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+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else { /* inlined PySequence_GetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
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+ }
+ return m->sq_item(o, i);
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}
- else {
- r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
}
- return r;
+#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
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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*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
-static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
-static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
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-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
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#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
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- }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
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static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
+
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname); /*proto*/
+
+#define __Pyx_CyFunction_USED 1
+#include <structmember.h>
+#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
+#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
+#define __Pyx_CYFUNCTION_CCLASS 0x04
+#define __Pyx_CyFunction_GetClosure(f) \
+ (((__pyx_CyFunctionObject *) (f))->func_closure)
+#define __Pyx_CyFunction_GetClassObj(f) \
+ (((__pyx_CyFunctionObject *) (f))->func_classobj)
+#define __Pyx_CyFunction_Defaults(type, f) \
+ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
+#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
+ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
+typedef struct {
+ PyCFunctionObject func;
+ int flags;
+ PyObject *func_dict;
+ PyObject *func_weakreflist;
+ PyObject *func_name;
+ PyObject *func_doc;
+ PyObject *func_code;
+ PyObject *func_closure;
+ PyObject *func_classobj; /* No-args super() class cell */
+ void *defaults;
+ int defaults_pyobjects;
+ PyObject *defaults_tuple; /* Const defaults tuple */
+ PyObject *(*defaults_getter)(PyObject *);
+} __pyx_CyFunctionObject;
+static PyTypeObject *__pyx_CyFunctionType = 0;
+#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \
+ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code)
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *,
+ PyMethodDef *ml, int flags,
+ PyObject *self, PyObject *module,
+ PyObject* code);
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
+ size_t size,
+ int pyobjects);
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
+ PyObject *tuple);
+static int __Pyx_CyFunction_init(void);
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+static int __Pyx_check_binary_version(void);
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
-static void __Pyx_AddTraceback(const char *funcname); /*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, int c_line,
+ int py_line, const char *filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from cpython.version */
-/* Module declarations from cpython.ref */
-/* Module declarations from cpython.exc */
+/* Module declarations from 'TabProxies' */
+static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0;
+static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0;
+static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0;
+static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0;
+static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
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+/* Module declarations from 'cpython.version' */
+
+/* Module declarations from 'cpython.ref' */
+
+/* Module declarations from 'cpython.exc' */
-/* Module declarations from cpython.module */
+/* Module declarations from 'cpython.module' */
-/* Module declarations from cpython.mem */
+/* Module declarations from 'cpython.mem' */
-/* Module declarations from cpython.tuple */
+/* Module declarations from 'cpython.tuple' */
-/* Module declarations from cpython.list */
+/* Module declarations from 'cpython.list' */
-/* Module declarations from libc.stdio */
+/* Module declarations from 'libc.stdio' */
-/* Module declarations from cpython.object */
+/* Module declarations from 'cpython.object' */
-/* Module declarations from cpython.sequence */
+/* Module declarations from 'cpython.sequence' */
-/* Module declarations from cpython.mapping */
+/* Module declarations from 'cpython.mapping' */
-/* Module declarations from cpython.iterator */
+/* Module declarations from 'cpython.iterator' */
-/* Module declarations from cpython.type */
+/* Module declarations from '__builtin__' */
-/* Module declarations from cpython.number */
+/* Module declarations from 'cpython.type' */
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+/* 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 */
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-/* 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 TabProxies */
+/* Module declarations from 'cpython.pycapsule' */
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-static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
-/* Module declarations from ctabix */
+/* Module declarations from 'cpython' */
+/* Module declarations from 'ctabix' */
static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0;
static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0;
static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0;
static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0;
static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0;
static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0;
static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0;
static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_tabix_inplace_iterator = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_tabix_copy_iterator = 0;
+static PyObject *__pyx_v_6ctabix__FILENAME_ENCODING = 0;
+static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_6ctabix__charptr_to_str(char *); /*proto*/
#define __Pyx_MODULE_NAME "ctabix"
-static int __pyx_module_is_main_ctabix = 0;
+int __pyx_module_is_main_ctabix = 0;
-/* Implementation of ctabix */
+/* Implementation of 'ctabix' */
+static PyObject *__pyx_builtin_TypeError;
+static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_OSError;
static PyObject *__pyx_builtin_ord;
static PyObject *__pyx_builtin_KeyError;
-static char __pyx_k_1[] = "invalid file opening mode `%s`";
-static char __pyx_k_2[] = ".tbi";
-static char __pyx_k_3[] = "file `%s` not found";
-static char __pyx_k_4[] = "index `%s` not found";
-static char __pyx_k_5[] = "could not open file `%s`";
-static char __pyx_k_6[] = "%s:%i-%i";
-static char __pyx_k_7[] = "invalid region `%s`";
-static char __pyx_k_8[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_9[] = "start out of range (%i)";
-static char __pyx_k_10[] = "end out of range (%i)";
-static char __pyx_k_11[] = "I/O operation on closed file";
-static char __pyx_k_14[] = "malformatted query or wrong sequence name.\n";
-static char __pyx_k_16[] = "can't open header.\n";
-static char __pyx_k_20[] = "Filename '%s' already exists, use *force* to overwrite";
-static char __pyx_k_21[] = "could not open '%s' for writing";
-static char __pyx_k_23[] = "could not open '%s' for reading";
-static char __pyx_k_25[] = "writing failed";
-static char __pyx_k_29[] = "#";
-static char __pyx_k_31[] = "No such file '%s'";
-static char __pyx_k_32[] = ".gz";
-static char __pyx_k_34[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
-static char __pyx_k_42[] = "unknown preset '%s', valid presets are '%s'";
-static char __pyx_k_43[] = ",";
-static char __pyx_k_44[] = "filename associated with this object.";
-static char __pyx_k_45[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
-static char __pyx_k_46[] = "chromosome names";
+static PyObject *__pyx_builtin_MemoryError;
+static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */
+static PyObject *__pyx_pf_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */
+static void __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */
+static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */
+static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
+static void __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
+static void __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */
+static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */
+static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
+static void __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
+static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* 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[] = "invalid file opening mode `%s`";
+static char __pyx_k_6[] = ".tbi";
+static char __pyx_k_7[] = "http:";
+static char __pyx_k_9[] = "ftp:";
+static char __pyx_k_12[] = "writing to tabix files not implemented";
+static char __pyx_k_14[] = "file `%s` not found";
+static char __pyx_k_15[] = "index `%s` not found";
+static char __pyx_k_16[] = "could not open file `%s`";
+static char __pyx_k_17[] = "%s:%i-%i";
+static char __pyx_k_18[] = "invalid region `%s`";
+static char __pyx_k_19[] = "invalid region: start (%i) > end (%i)";
+static char __pyx_k_20[] = "start out of range (%i)";
+static char __pyx_k_21[] = "end out of range (%i)";
+static char __pyx_k_22[] = "I/O operation on closed file";
+static char __pyx_k_25[] = "malformatted query or wrong sequence name.\n";
+static char __pyx_k_27[] = "can't open header.\n";
+static char __pyx_k_31[] = "Filename '%s' already exists, use *force* to overwrite";
+static char __pyx_k_32[] = "could not open '%s' for writing";
+static char __pyx_k_34[] = "could not open '%s' for reading";
+static char __pyx_k_36[] = "writing failed";
+static char __pyx_k_40[] = "#";
+static char __pyx_k_42[] = "No such file '%s'";
+static char __pyx_k_43[] = ".gz";
+static char __pyx_k_45[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
+static char __pyx_k_47[] = "unknown preset '%s', valid presets are '%s'";
+static char __pyx_k_48[] = ",";
+static char __pyx_k_49[] = "I/O operation on closed file.";
+static char __pyx_k_52[] = "incomplete line at %s";
+static char __pyx_k_56[] = "tabix_generic_iterator";
+static char __pyx_k_57[] = "filename associated with this object.";
+static char __pyx_k_58[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
+static char __pyx_k_59[] = "chromosome names";
+static char __pyx_k_60[] = "getfilesystemencoding";
+static char __pyx_k_63[] = "/ifs/devel/pysam/pysam/ctabix.pyx";
+static char __pyx_k_74[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
+static char __pyx_k_77[] = "tabix_inplace_iterator";
+static char __pyx_k__b[] = "b";
+static char __pyx_k__c[] = "c";
static char __pyx_k__r[] = "r";
+static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
-static char __pyx_k__bc[] = "bc";
-static char __pyx_k__ec[] = "ec";
+static char __pyx_k__fn[] = "fn";
static char __pyx_k__fp[] = "fp";
+static char __pyx_k__io[] = "io";
static char __pyx_k__os[] = "os";
-static char __pyx_k__sc[] = "sc";
static char __pyx_k__bed[] = "bed";
+static char __pyx_k__cpy[] = "cpy";
static char __pyx_k__end[] = "end";
static char __pyx_k__gff[] = "gff";
-static char __pyx_k__idx[] = "idx";
static char __pyx_k__len[] = "len";
static char __pyx_k__ord[] = "ord";
static char __pyx_k__sam[] = "sam";
static char __pyx_k__sys[] = "sys";
static char __pyx_k__tid[] = "tid";
static char __pyx_k__vcf[] = "vcf";
-static char __pyx_k__copy[] = "copy";
+static char __pyx_k__conf[] = "conf";
static char __pyx_k__gzip[] = "gzip";
static char __pyx_k__join[] = "join";
-static char __pyx_k__keys[] = "keys";
+static char __pyx_k__line[] = "line";
static char __pyx_k__mode[] = "mode";
+static char __pyx_k__next[] = "next";
static char __pyx_k__path[] = "path";
+static char __pyx_k__self[] = "self";
static char __pyx_k___open[] = "_open";
static char __pyx_k__asBed[] = "asBed";
static char __pyx_k__asGTF[] = "asGTF";
static char __pyx_k__asVCF[] = "asVCF";
+static char __pyx_k__ascii[] = "ascii";
static char __pyx_k__close[] = "close";
static char __pyx_k__force[] = "force";
static char __pyx_k__start[] = "start";
static char __pyx_k__types[] = "types";
-static char __pyx_k__append[] = "append";
+static char __pyx_k__Parser[] = "Parser";
static char __pyx_k__buffer[] = "buffer";
+static char __pyx_k__closed[] = "closed";
static char __pyx_k__ctabix[] = "ctabix";
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__fd_src[] = "fd_src";
+static char __pyx_k__infile[] = "infile";
+static char __pyx_k__nbytes[] = "nbytes";
static char __pyx_k__parser[] = "parser";
static char __pyx_k__pileup[] = "pileup";
static char __pyx_k__preset[] = "preset";
static char __pyx_k__unlink[] = "unlink";
static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__OSError[] = "OSError";
+static char __pyx_k__PYTHON3[] = "PYTHON3";
static char __pyx_k____all__[] = "__all__";
static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k__asTuple[] = "asTuple";
static char __pyx_k__end_col[] = "end_col";
+static char __pyx_k__present[] = "present";
static char __pyx_k__seq_col[] = "seq_col";
static char __pyx_k__KeyError[] = "KeyError";
static char __pyx_k__O_RDONLY[] = "O_RDONLY";
+static char __pyx_k____init__[] = "__init__";
+static char __pyx_k____iter__[] = "__iter__";
static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__endswith[] = "endswith";
static char __pyx_k__filename[] = "filename";
-static char __pyx_k__iterator[] = "iterator";
+static char __pyx_k__readline[] = "readline";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__Tabixfile[] = "Tabixfile";
-static char __pyx_k___filename[] = "_filename";
+static char __pyx_k__TypeError[] = "TypeError";
+static char __pyx_k__conf_data[] = "conf_data";
static char __pyx_k__itertools[] = "itertools";
-static char __pyx_k__line_skip[] = "line_skip";
static char __pyx_k__meta_char[] = "meta_char";
static char __pyx_k__reference[] = "reference";
static char __pyx_k__start_col[] = "start_col";
static char __pyx_k__tabixfile[] = "tabixfile";
static char __pyx_k__zerobased[] = "zerobased";
static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k__startswith[] = "startswith";
+static char __pyx_k__MemoryError[] = "MemoryError";
+static char __pyx_k__WINDOW_SIZE[] = "WINDOW_SIZE";
+static char __pyx_k__buffer_size[] = "buffer_size";
static char __pyx_k__filename_in[] = "filename_in";
+static char __pyx_k__preset2conf[] = "preset2conf";
static char __pyx_k__tabix_index[] = "tabix_index";
static char __pyx_k___parseRegion[] = "_parseRegion";
static char __pyx_k__filename_out[] = "filename_out";
static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__tabix_compress[] = "tabix_compress";
-static PyObject *__pyx_kp_s_1;
-static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_11;
+static char __pyx_k__tabix_iterator[] = "tabix_iterator";
+static char __pyx_k__getdefaultencoding[] = "getdefaultencoding";
+static char __pyx_k__NotImplementedError[] = "NotImplementedError";
+static PyObject *__pyx_kp_u_1;
+static PyObject *__pyx_kp_s_12;
static PyObject *__pyx_kp_s_14;
+static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_16;
-static PyObject *__pyx_kp_s_2;
+static PyObject *__pyx_kp_s_17;
+static PyObject *__pyx_kp_s_18;
+static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_20;
static PyObject *__pyx_kp_s_21;
-static PyObject *__pyx_kp_s_23;
+static PyObject *__pyx_kp_s_22;
static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_3;
+static PyObject *__pyx_kp_s_27;
+static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_kp_s_32;
static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_4;
+static PyObject *__pyx_kp_s_36;
+static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
+static PyObject *__pyx_kp_s_45;
+static PyObject *__pyx_kp_s_47;
+static PyObject *__pyx_kp_s_48;
+static PyObject *__pyx_kp_s_49;
static PyObject *__pyx_kp_s_5;
+static PyObject *__pyx_kp_s_52;
+static PyObject *__pyx_n_s_56;
static PyObject *__pyx_kp_s_6;
+static PyObject *__pyx_n_s_60;
+static PyObject *__pyx_kp_s_63;
static PyObject *__pyx_kp_s_7;
-static PyObject *__pyx_kp_s_8;
+static PyObject *__pyx_kp_s_74;
+static PyObject *__pyx_n_s_77;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__KeyError;
+static PyObject *__pyx_n_s__MemoryError;
+static PyObject *__pyx_n_s__NotImplementedError;
static PyObject *__pyx_n_s__OSError;
static PyObject *__pyx_n_s__O_RDONLY;
+static PyObject *__pyx_n_s__PYTHON3;
+static PyObject *__pyx_n_s__Parser;
static PyObject *__pyx_n_s__StopIteration;
static PyObject *__pyx_n_s__Tabixfile;
+static PyObject *__pyx_n_s__TypeError;
static PyObject *__pyx_n_s__ValueError;
+static PyObject *__pyx_n_s__WINDOW_SIZE;
static PyObject *__pyx_n_s____all__;
+static PyObject *__pyx_n_s____init__;
+static PyObject *__pyx_n_s____iter__;
static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____next__;
static PyObject *__pyx_n_s____test__;
-static PyObject *__pyx_n_s___filename;
static PyObject *__pyx_n_s___isOpen;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
-static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__asBed;
static PyObject *__pyx_n_s__asGTF;
static PyObject *__pyx_n_s__asTuple;
static PyObject *__pyx_n_s__asVCF;
-static PyObject *__pyx_n_s__bc;
+static PyObject *__pyx_n_s__ascii;
+static PyObject *__pyx_n_s__b;
static PyObject *__pyx_n_s__bed;
static PyObject *__pyx_n_s__buffer;
+static PyObject *__pyx_n_s__buffer_size;
+static PyObject *__pyx_n_s__c;
static PyObject *__pyx_n_s__close;
-static PyObject *__pyx_n_s__copy;
+static PyObject *__pyx_n_s__closed;
+static PyObject *__pyx_n_s__conf;
+static PyObject *__pyx_n_s__conf_data;
+static PyObject *__pyx_n_s__cpy;
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+ {(char *)"header", __pyx_getprop_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_58), 0},
+ {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_59), 0},
+ {0, 0, 0, 0, 0}
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+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_Tabixfile = {
+ 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_Tabixfile = {
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+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
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+static PyBufferProcs __pyx_tp_as_buffer_Tabixfile = {
+ #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
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+ __Pyx_NAMESTR("ctabix.Tabixfile"), /*tp_name*/
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+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_6ctabix_Tabixfile, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
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+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_Tabixfile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Tabixfile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Tabixfile, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_Tabixfile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename, mode='r')*\n\n opens a :term:`tabix file` for reading. A missing\n index (*filename* + \".tbi\") will raise an exception.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_6ctabix_Tabixfile, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_6ctabix_Tabixfile, /*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_6ctabix_Tabixfile, /*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
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+static PyObject *__pyx_tp_new_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
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+ if (__pyx_pw_6ctabix_13TabixIterator_1__cinit__(o, a, k) < 0) {
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+}
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+static void __pyx_tp_dealloc_6ctabix_TabixIterator(PyObject *o) {
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+ ++Py_REFCNT(o);
+ __pyx_pw_6ctabix_13TabixIterator_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
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+ {0, 0, 0, 0}
+};
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+static PyNumberMethods __pyx_tp_as_number_TabixIterator = {
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+ 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*/
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+ 0, /*reserved*/
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+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_TabixIterator = {
+ 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*/
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+static PyMappingMethods __pyx_tp_as_mapping_TabixIterator = {
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+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
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+ #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*/
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+ #if PY_VERSION_HEX >= 0x02060000
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- __Pyx_XGIVEREF(__pyx_r);
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+static PyTypeObject __pyx_type_6ctabix_TabixIterator = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("ctabix.TabixIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_TabixIterator), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_6ctabix_TabixIterator, /*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_TabixIterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixIterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TabixIterator, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_TabixIterator, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ __pyx_pw_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/
+ __pyx_pw_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/
+ __pyx_methods_6ctabix_TabixIterator, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_6ctabix_TabixIterator, /*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_6ctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- if (__pyx_pf_6ctabix_9Tabixfile___cinit__(o, a, k) < 0) {
+ if (__pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_Tabixfile(PyObject *o) {
+static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_6ctabix_9Tabixfile_6__dealloc__(o);
+ __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
(*Py_TYPE(o)->tp_free)(o);
}
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-
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-
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- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_6ctabix_9Tabixfile_5close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_5close)},
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+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixHeaderIterator_4__next__)},
{0, 0, 0, 0}
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- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Tabixfile = {
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0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Tabixfile = {
+static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_Tabixfile = {
+static PyMappingMethods __pyx_tp_as_mapping_TabixHeaderIterator = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Tabixfile = {
+static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_Tabixfile = {
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PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.Tabixfile"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_Tabixfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.TabixHeaderIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Tabixfile, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
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- &__pyx_tp_as_sequence_Tabixfile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Tabixfile, /*tp_as_mapping*/
+ &__pyx_tp_as_number_TabixHeaderIterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/
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0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Tabixfile, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("*(filename, mode='r')*\n\n opens a :term:`tabix file` for reading. A missing\n index (*filename* + \".tbi\") will raise an exception.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_6ctabix_Tabixfile, /*tp_methods*/
+ __pyx_pw_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/
+ __pyx_pw_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/
+ __pyx_methods_6ctabix_TabixHeaderIterator, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_6ctabix_Tabixfile, /*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_6ctabix_Tabixfile, /*tp_new*/
+ __pyx_tp_new_6ctabix_TabixHeaderIterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
- if (__pyx_pf_6ctabix_13TabixIterator___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TabixIterator(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_6ctabix_13TabixIterator_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- (*Py_TYPE(o)->tp_free)(o);
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-
-static PyMethodDef __pyx_methods_6ctabix_TabixIterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_6ctabix_13TabixIterator_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_13TabixIterator_2__next__)},
+static PyMethodDef __pyx_methods_6ctabix_asTuple[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_TabixIterator = {
+static PyNumberMethods __pyx_tp_as_number_asTuple = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_TabixIterator = {
+static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_TabixIterator = {
+static PyMappingMethods __pyx_tp_as_mapping_asTuple = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_TabixIterator = {
+static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixIterator = {
+static PyTypeObject __pyx_type_6ctabix_asTuple = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.TabixIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_TabixIterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TabixIterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TabixIterator, /*tp_as_number*/
- &__pyx_tp_as_sequence_TabixIterator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TabixIterator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asTuple, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
0, /*tp_hash*/
- 0, /*tp_call*/
+ __pyx_pw_6ctabix_7asTuple_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TabixIterator, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("iterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_6ctabix_13TabixIterator_1__iter__, /*tp_iter*/
- __pyx_pf_6ctabix_13TabixIterator_2__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TabixIterator, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_6ctabix_asTuple, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TabixIterator, /*tp_new*/
+ __pyx_tp_new_6ctabix_asTuple, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
- if (__pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_6ctabix_19TabixHeaderIterator_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static PyMethodDef __pyx_methods_6ctabix_TabixHeaderIterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_6ctabix_19TabixHeaderIterator_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixHeaderIterator_2__next__)},
+static PyMethodDef __pyx_methods_6ctabix_asGTF[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = {
+static PyNumberMethods __pyx_tp_as_number_asGTF = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = {
+static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_TabixHeaderIterator = {
+static PyMappingMethods __pyx_tp_as_mapping_asGTF = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
+static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
+static PyTypeObject __pyx_type_6ctabix_asGTF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.TabixHeaderIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TabixHeaderIterator, /*tp_as_number*/
- &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TabixHeaderIterator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asGTF, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
0, /*tp_hash*/
- 0, /*tp_call*/
+ __pyx_pw_6ctabix_5asGTF_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record with the following \n fields:\n\n contig\n contig\n feature\n feature\n source\n source\n start\n genomic start coordinate (0-based)\n end\n genomic end coordinate plus one (0-based)\n score\n feature score\n strand\n strand\n frame\n frame\n attributes\n attribute string.\n\n GTF formatted entries also defined the attributes:\n\n gene_id\n the gene identifier\n transcript_ind\n the transcript identifier\n \n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_6ctabix_19TabixHeaderIterator_1__iter__, /*tp_iter*/
- __pyx_pf_6ctabix_19TabixHeaderIterator_2__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TabixHeaderIterator, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_6ctabix_asGTF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TabixHeaderIterator, /*tp_new*/
+ __pyx_tp_new_6ctabix_asGTF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asTuple[] = {
+static PyMethodDef __pyx_methods_6ctabix_asBed[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asTuple = {
+static PyNumberMethods __pyx_tp_as_number_asBed = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
+static PySequenceMethods __pyx_tp_as_sequence_asBed = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asTuple = {
+static PyMappingMethods __pyx_tp_as_mapping_asBed = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
+static PyBufferProcs __pyx_tp_as_buffer_asBed = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asTuple = {
+static PyTypeObject __pyx_type_6ctabix_asBed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asBed"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asBed), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asTuple, /*tp_as_number*/
- &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asBed, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_6ctabix_7asTuple___call__, /*tp_call*/
+ __pyx_pw_6ctabix_5asBed_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n contig\n contig\n start\n genomic start coordinate (zero-based)\n end\n genomic end coordinate plus one (zero-based)\n name\n name of feature.\n score\n score of feature\n strand\n strand of feature\n thickStart\n thickStart\n thickEnd\n thickEnd\n itemRGB\n itemRGB\n blockCount\n number of bocks\n blockSizes\n ',' separated string of block sizes\n blockStarts\n ',' separated string of block genomic start positions\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceeding\n need to be defined as well.\n\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asTuple, /*tp_methods*/
+ __pyx_methods_6ctabix_asBed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asTuple, /*tp_new*/
+ __pyx_tp_new_6ctabix_asBed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asGTF[] = {
+static PyMethodDef __pyx_methods_6ctabix_asVCF[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asGTF = {
+static PyNumberMethods __pyx_tp_as_number_asVCF = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
+static PySequenceMethods __pyx_tp_as_sequence_asVCF = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asGTF = {
+static PyMappingMethods __pyx_tp_as_mapping_asVCF = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
+static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asGTF = {
+static PyTypeObject __pyx_type_6ctabix_asVCF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asVCF"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asVCF), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asGTF, /*tp_as_number*/
- &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asVCF, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_6ctabix_5asGTF___call__, /*tp_call*/
+ __pyx_pw_6ctabix_5asVCF_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record with the following \n fields:\n\n contig\n contig\n feature\n feature\n source\n source\n start\n genomic start coordinate (0-based)\n end\n genomic end coordinate plus one (0-based)\n score\n feature score\n strand\n strand\n frame\n frame\n attributes\n attribute string.\n\n GTF formatted entries also defined the attributes:\n\n gene_id\n the gene identifier\n transcript_ind\n the transcript identifier\n \n "), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n contig\n contig\n pos\n chromosomal position, zero-based\n id \n id\n ref\n reference\n alt\n alt\n qual\n qual\n filter\n filter\n info\n info\n format\n format specifier.\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asGTF, /*tp_methods*/
+ __pyx_methods_6ctabix_asVCF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asGTF, /*tp_new*/
+ __pyx_tp_new_6ctabix_asVCF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_6ctabix_TabixIteratorParsed *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ p = ((struct __pyx_obj_6ctabix_TabixIteratorParsed *)o);
+ p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asBed[] = {
+static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) {
+ struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_6ctabix_19TabixIteratorParsed_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->parser);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+ if (p->parser) {
+ e = (*v)(((PyObject*)p->parser), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_6ctabix_TabixIteratorParsed(PyObject *o) {
+ struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->parser);
+ p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_6ctabix_TabixIteratorParsed[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixIteratorParsed_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asBed = {
+static PyNumberMethods __pyx_tp_as_number_TabixIteratorParsed = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asBed = {
+static PySequenceMethods __pyx_tp_as_sequence_TabixIteratorParsed = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asBed = {
+static PyMappingMethods __pyx_tp_as_mapping_TabixIteratorParsed = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asBed = {
+static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asBed = {
+static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asBed"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asBed), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.TabixIteratorParsed"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asBed, /*tp_as_number*/
- &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/
+ &__pyx_tp_as_number_TabixIteratorParsed, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixIteratorParsed, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TabixIteratorParsed, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_6ctabix_5asBed___call__, /*tp_call*/
+ 0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n contig\n contig\n start\n genomic start coordinate (zero-based)\n end\n genomic end coordinate plus one (zero-based)\n name\n name of feature.\n score\n score of feature\n strand\n strand of feature\n thickStart\n thickStart\n thickEnd\n thickEnd\n itemRGB\n itemRGB\n blockCount\n number of bocks\n blockSizes\n ',' separated string of block sizes\n blockStarts\n ',' separated string of block genomic start positions\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceeding\n need to be defined as well.\n\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_TabixIteratorParsed, /*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 mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/
+ __pyx_tp_traverse_6ctabix_TabixIteratorParsed, /*tp_traverse*/
+ __pyx_tp_clear_6ctabix_TabixIteratorParsed, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_6ctabix_asBed, /*tp_methods*/
+ __pyx_pw_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/
+ __pyx_pw_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/
+ __pyx_methods_6ctabix_TabixIteratorParsed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asBed, /*tp_new*/
+ __pyx_tp_new_6ctabix_TabixIteratorParsed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator __pyx_vtable_6ctabix_tabix_inplace_iterator;
-static PyObject *__pyx_tp_new_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_6ctabix_tabix_inplace_iterator *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ p = ((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o);
+ p->__pyx_vtab = __pyx_vtabptr_6ctabix_tabix_inplace_iterator;
+ p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asVCF[] = {
+static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) {
+ struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->parser);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+ if (p->parser) {
+ e = (*v)(((PyObject*)p->parser), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_6ctabix_tabix_inplace_iterator(PyObject *o) {
+ struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->parser);
+ p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_6ctabix_tabix_inplace_iterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asVCF = {
+static PyNumberMethods __pyx_tp_as_number_tabix_inplace_iterator = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asVCF = {
+static PySequenceMethods __pyx_tp_as_sequence_tabix_inplace_iterator = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asVCF = {
+static PyMappingMethods __pyx_tp_as_mapping_tabix_inplace_iterator = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
+static PyBufferProcs __pyx_tp_as_buffer_tabix_inplace_iterator = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asVCF = {
+static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asVCF"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asVCF), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.tabix_inplace_iterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asVCF, /*tp_as_number*/
- &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/
+ &__pyx_tp_as_number_tabix_inplace_iterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_tabix_inplace_iterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_tabix_inplace_iterator, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_6ctabix_5asVCF___call__, /*tp_call*/
+ 0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n contig\n contig\n pos\n chromosomal position, zero-based\n id \n id\n ref\n reference\n alt\n alt\n qual\n qual\n filter\n filter\n info\n info\n format\n format specifier.\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_tabix_inplace_iterator, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not safe. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/
+ __pyx_tp_traverse_6ctabix_tabix_inplace_iterator, /*tp_traverse*/
+ __pyx_tp_clear_6ctabix_tabix_inplace_iterator, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_6ctabix_asVCF, /*tp_methods*/
+ __pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/
+ __pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/
+ __pyx_methods_6ctabix_tabix_inplace_iterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asVCF, /*tp_new*/
+ __pyx_tp_new_6ctabix_tabix_inplace_iterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator __pyx_vtable_6ctabix_tabix_copy_iterator;
-static PyObject *__pyx_tp_new_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p;
+static PyObject *__pyx_tp_new_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_6ctabix_tabix_copy_iterator *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_6ctabix_TabixIteratorParsed *)o);
+ p = ((struct __pyx_obj_6ctabix_tabix_copy_iterator *)o);
+ p->__pyx_vtab = __pyx_vtabptr_6ctabix_tabix_copy_iterator;
p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(o, a, k) < 0) {
+ if (__pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) {
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_6ctabix_19TabixIteratorParsed_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_XDECREF(((PyObject *)p->parser));
+static void __pyx_tp_dealloc_6ctabix_tabix_copy_iterator(PyObject *o) {
+ struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
+ Py_CLEAR(p->parser);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+ struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
if (p->parser) {
e = (*v)(((PyObject*)p->parser), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_6ctabix_TabixIteratorParsed(PyObject *o) {
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+static int __pyx_tp_clear_6ctabix_tabix_copy_iterator(PyObject *o) {
+ struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
PyObject* tmp;
tmp = ((PyObject*)p->parser);
p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
return 0;
}
-static PyMethodDef __pyx_methods_6ctabix_TabixIteratorParsed[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_6ctabix_19TabixIteratorParsed_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixIteratorParsed_2__next__)},
+static PyMethodDef __pyx_methods_6ctabix_tabix_copy_iterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_TabixIteratorParsed = {
+static PyNumberMethods __pyx_tp_as_number_tabix_copy_iterator = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_TabixIteratorParsed = {
+static PySequenceMethods __pyx_tp_as_sequence_tabix_copy_iterator = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_TabixIteratorParsed = {
+static PyMappingMethods __pyx_tp_as_mapping_tabix_copy_iterator = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = {
+static PyBufferProcs __pyx_tp_as_buffer_tabix_copy_iterator = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
+static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.TabixIteratorParsed"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.tabix_copy_iterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_tabix_copy_iterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_tabix_copy_iterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TabixIteratorParsed, /*tp_as_number*/
- &__pyx_tp_as_sequence_TabixIteratorParsed, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TabixIteratorParsed, /*tp_as_mapping*/
+ &__pyx_tp_as_number_tabix_copy_iterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_tabix_copy_iterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_tabix_copy_iterator, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TabixIteratorParsed, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_tabix_copy_iterator, /*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 mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/
- __pyx_tp_traverse_6ctabix_TabixIteratorParsed, /*tp_traverse*/
- __pyx_tp_clear_6ctabix_TabixIteratorParsed, /*tp_clear*/
+ __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not save. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/
+ __pyx_tp_traverse_6ctabix_tabix_copy_iterator, /*tp_traverse*/
+ __pyx_tp_clear_6ctabix_tabix_copy_iterator, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_6ctabix_19TabixIteratorParsed_1__iter__, /*tp_iter*/
- __pyx_pf_6ctabix_19TabixIteratorParsed_2__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TabixIteratorParsed, /*tp_methods*/
+ __pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__, /*tp_iter*/
+ __pyx_pw_6ctabix_19tabix_copy_iterator_5__next__, /*tp_iternext*/
+ __pyx_methods_6ctabix_tabix_copy_iterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TabixIteratorParsed, /*tp_new*/
+ __pyx_tp_new_6ctabix_tabix_copy_iterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
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+ if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Constants init code ---*/
if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
+ __pyx_v_6ctabix__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ /*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- if (PyType_Ready(&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_Tabixfile = &__pyx_type_6ctabix_Tabixfile;
- if (PyType_Ready(&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Parser", (PyObject *)&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_Parser = &__pyx_type_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_6ctabix_13TabixIterator_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_6ctabix_13TabixIterator_2__next__.doc = __pyx_doc_6ctabix_13TabixIterator_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_13TabixIterator_2__next__;
+ __pyx_wrapperbase_6ctabix_13TabixIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_6ctabix_13TabixIterator_4__next__.doc = __pyx_doc_6ctabix_13TabixIterator_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_13TabixIterator_4__next__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_TabixIterator = &__pyx_type_6ctabix_TabixIterator;
- if (PyType_Ready(&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_2__next__.doc = __pyx_doc_6ctabix_19TabixHeaderIterator_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixHeaderIterator_2__next__;
+ __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__.doc = __pyx_doc_6ctabix_19TabixHeaderIterator_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_TabixHeaderIterator = &__pyx_type_6ctabix_TabixHeaderIterator;
+ if (PyType_Ready(&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Parser", (PyObject *)&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_6ctabix_Parser = &__pyx_type_6ctabix_Parser;
__pyx_type_6ctabix_asTuple.tp_base = __pyx_ptype_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asTuple", (PyObject *)&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asTuple", (PyObject *)&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_asTuple = &__pyx_type_6ctabix_asTuple;
__pyx_type_6ctabix_asGTF.tp_base = __pyx_ptype_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_asGTF = &__pyx_type_6ctabix_asGTF;
__pyx_type_6ctabix_asBed.tp_base = __pyx_ptype_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_asBed = &__pyx_type_6ctabix_asBed;
__pyx_type_6ctabix_asVCF.tp_base = __pyx_ptype_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_asVCF = &__pyx_type_6ctabix_asVCF;
- if (PyType_Ready(&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_2__next__.doc = __pyx_doc_6ctabix_19TabixIteratorParsed_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed_2__next__;
+ __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__.doc = __pyx_doc_6ctabix_19TabixIteratorParsed_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_TabixIteratorParsed = &__pyx_type_6ctabix_TabixIteratorParsed;
+ __pyx_vtabptr_6ctabix_tabix_inplace_iterator = &__pyx_vtable_6ctabix_tabix_inplace_iterator;
+ __pyx_vtable_6ctabix_tabix_inplace_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *))__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__;
+ if (PyType_Ready(&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_6ctabix_tabix_inplace_iterator = &__pyx_type_6ctabix_tabix_inplace_iterator;
+ __pyx_vtabptr_6ctabix_tabix_copy_iterator = &__pyx_vtable_6ctabix_tabix_copy_iterator;
+ __pyx_vtable_6ctabix_tabix_copy_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_copy_iterator *))__pyx_f_6ctabix_19tabix_copy_iterator___cnext__;
+ if (PyType_Ready(&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_6ctabix_tabix_copy_iterator = &__pyx_type_6ctabix_tabix_copy_iterator;
/*--- Type import code ---*/
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
-
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;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
}
#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) {
+ PyObject* owned_instance = NULL;
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,
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
-
+ if (cause && cause != Py_None) {
+ 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;
+ }
+ 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:
+ Py_XDECREF(owned_instance);
return;
}
#endif
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "need more than %d value%s to unpack", (int)index,
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
- "need more than %zd value%s to unpack", index,
+ "%s() got multiple values for keyword argument '%s'", func_name,
+ PyString_AsString(kw_name));
+ #endif
+}
+
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
+ PyObject *key = 0, *value = 0;
+ 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 (*name) {
+ values[name-argnames] = value;
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
+ }
+ argname++;
+ }
+ }
+ } else
#endif
- (index == 1) ? "" : "s");
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
+ }
+ }
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ goto bad;
+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
+bad:
+ return -1;
+}
+
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *more_or_less;
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ PyErr_Format(PyExc_TypeError,
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ func_name, more_or_less, num_expected,
+ (num_expected == 1) ? "" : "s", num_found);
}
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
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ index, (index == 1) ? "" : "s");
}
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
- PyObject *item;
- if (!(item = PyIter_Next(iter))) {
- if (!PyErr_Occurred()) {
- __Pyx_RaiseNeedMoreValuesError(index);
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
}
}
- return item;
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
}
-static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
- PyObject *item;
- if ((item = PyIter_Next(iter))) {
- Py_DECREF(item);
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
+ } else {
+ return __Pyx_IterFinish();
}
- else if (!PyErr_Occurred())
- return 0;
- else
- return -1;
+ return 0;
}
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
return 0;
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
-}
-
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- #endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
+ goto bad;
+ #endif
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
return -1;
}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
-
static void __Pyx_ExceptionReset(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->exc_type;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
-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,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ }
+ }
+ #else
+ if (level>0) {
+ PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
+ goto bad;
+ }
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, NULL);
+ #endif
bad:
Py_XDECREF(empty_list);
Py_XDECREF(py_import);
return module;
}
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
+ PyObject *metaclass;
+#if PY_MAJOR_VERSION < 3
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = PyObject_GetAttrString(base, (char *)"__class__");
+ if (!metaclass) {
+ PyErr_Clear();
+ metaclass = (PyObject*) Py_TYPE(base);
+ }
+ } else {
+ metaclass = (PyObject *) &PyClass_Type;
+ }
+#else
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = (PyObject*) Py_TYPE(base);
+ } else {
+ metaclass = (PyObject *) &PyType_Type;
+ }
+#endif
+ Py_INCREF(metaclass);
+ return metaclass;
+}
+
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname) {
+ PyObject *result;
+ PyObject *metaclass;
+ if (PyDict_SetItemString(dict, "__module__", modname) < 0)
+ return NULL;
+ metaclass = PyDict_GetItemString(dict, "__metaclass__");
+ if (metaclass) {
+ Py_INCREF(metaclass);
+ } else {
+ metaclass = __Pyx_FindPy2Metaclass(bases);
+ }
+ result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
+ Py_DECREF(metaclass);
+ return result;
+}
+
+static PyObject *
+__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
+{
+ if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
+#if PY_MAJOR_VERSION >= 3
+ op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
+#else
+ op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
+#endif
+ }
+ if (op->func_doc == 0) {
+ Py_INCREF(Py_None);
+ return Py_None;
+ }
+ Py_INCREF(op->func_doc);
+ return op->func_doc;
+}
+static int
+__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp = op->func_doc;
+ if (value == NULL)
+ op->func_doc = Py_None; /* Mark as deleted */
+ else
+ op->func_doc = value;
+ Py_INCREF(op->func_doc);
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
+{
+ if (op->func_name == NULL) {
+#if PY_MAJOR_VERSION >= 3
+ op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
+#else
+ op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
+#endif
+ }
+ Py_INCREF(op->func_name);
+ return op->func_name;
+}
+static int
+__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+ if (value == NULL || !PyUnicode_Check(value)) {
+#else
+ if (value == NULL || !PyString_Check(value)) {
+#endif
+ PyErr_SetString(PyExc_TypeError,
+ "__name__ must be set to a string object");
+ return -1;
+ }
+ tmp = op->func_name;
+ Py_INCREF(value);
+ op->func_name = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
+{
+ PyObject *self;
+ self = m->func_closure;
+ if (self == NULL)
+ self = Py_None;
+ Py_INCREF(self);
+ return self;
+}
+static PyObject *
+__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
+{
+ if (op->func_dict == NULL) {
+ op->func_dict = PyDict_New();
+ if (op->func_dict == NULL)
+ return NULL;
+ }
+ Py_INCREF(op->func_dict);
+ return op->func_dict;
+}
+static int
+__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+ if (value == NULL) {
+ PyErr_SetString(PyExc_TypeError,
+ "function's dictionary may not be deleted");
+ return -1;
+ }
+ if (!PyDict_Check(value)) {
+ PyErr_SetString(PyExc_TypeError,
+ "setting function's dictionary to a non-dict");
+ return -1;
+ }
+ tmp = op->func_dict;
+ Py_INCREF(value);
+ op->func_dict = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+ PyObject* dict = PyModule_GetDict(__pyx_m);
+ Py_XINCREF(dict);
+ return dict;
+}
+static PyObject *
+__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+static PyObject *
+__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
+{
+ PyObject* result = (op->func_code) ? op->func_code : Py_None;
+ Py_INCREF(result);
+ return result;
+}
+static PyObject *
+__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
+{
+ if (op->defaults_tuple) {
+ Py_INCREF(op->defaults_tuple);
+ return op->defaults_tuple;
+ }
+ if (op->defaults_getter) {
+ PyObject *res = op->defaults_getter((PyObject *) op);
+ if (res) {
+ Py_INCREF(res);
+ op->defaults_tuple = res;
+ }
+ return res;
+ }
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+static PyGetSetDef __pyx_CyFunction_getsets[] = {
+ {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+ {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+ {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
+ {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+ {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+ {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+ {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+ {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+ {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+ {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+ {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+ {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+ {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
+#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
+#endif
+static PyMemberDef __pyx_CyFunction_members[] = {
+ {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
+ {0, 0, 0, 0, 0}
+};
+static PyObject *
+__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
+{
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_FromString(m->func.m_ml->ml_name);
+#else
+ return PyString_FromString(m->func.m_ml->ml_name);
+#endif
+}
+static PyMethodDef __pyx_CyFunction_methods[] = {
+ {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
+ {0, 0, 0, 0}
+};
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
+ PyObject *closure, PyObject *module, PyObject* code) {
+ __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
+ if (op == NULL)
+ return NULL;
+ op->flags = flags;
+ op->func_weakreflist = NULL;
+ op->func.m_ml = ml;
+ op->func.m_self = (PyObject *) op;
+ Py_XINCREF(closure);
+ op->func_closure = closure;
+ Py_XINCREF(module);
+ op->func.m_module = module;
+ op->func_dict = NULL;
+ op->func_name = NULL;
+ op->func_doc = NULL;
+ op->func_classobj = NULL;
+ Py_XINCREF(code);
+ op->func_code = code;
+ op->defaults_pyobjects = 0;
+ op->defaults = NULL;
+ op->defaults_tuple = NULL;
+ op->defaults_getter = NULL;
+ PyObject_GC_Track(op);
+ return (PyObject *) op;
+}
+static int
+__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
+{
+ Py_CLEAR(m->func_closure);
+ Py_CLEAR(m->func.m_module);
+ Py_CLEAR(m->func_dict);
+ Py_CLEAR(m->func_name);
+ Py_CLEAR(m->func_doc);
+ Py_CLEAR(m->func_code);
+ Py_CLEAR(m->func_classobj);
+ Py_CLEAR(m->defaults_tuple);
+ if (m->defaults) {
+ PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+ int i;
+ for (i = 0; i < m->defaults_pyobjects; i++)
+ Py_XDECREF(pydefaults[i]);
+ PyMem_Free(m->defaults);
+ m->defaults = NULL;
+ }
+ return 0;
+}
+static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
+{
+ PyObject_GC_UnTrack(m);
+ if (m->func_weakreflist != NULL)
+ PyObject_ClearWeakRefs((PyObject *) m);
+ __Pyx_CyFunction_clear(m);
+ PyObject_GC_Del(m);
+}
+static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
+{
+ Py_VISIT(m->func_closure);
+ Py_VISIT(m->func.m_module);
+ Py_VISIT(m->func_dict);
+ Py_VISIT(m->func_name);
+ Py_VISIT(m->func_doc);
+ Py_VISIT(m->func_code);
+ Py_VISIT(m->func_classobj);
+ Py_VISIT(m->defaults_tuple);
+ if (m->defaults) {
+ PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+ int i;
+ for (i = 0; i < m->defaults_pyobjects; i++)
+ Py_VISIT(pydefaults[i]);
+ }
+ return 0;
+}
+static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
+{
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
+ Py_INCREF(func);
+ return func;
+ }
+ if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
+ if (type == NULL)
+ type = (PyObject *)(Py_TYPE(obj));
+ return PyMethod_New(func,
+ type, (PyObject *)(Py_TYPE(type)));
+ }
+ if (obj == Py_None)
+ obj = NULL;
+ return PyMethod_New(func, obj, type);
+}
+static PyObject*
+__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
+{
+ PyObject *func_name = __Pyx_CyFunction_get_name(op);
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_FromFormat("<cyfunction %U at %p>",
+ func_name, (void *)op);
+#else
+ return PyString_FromFormat("<cyfunction %s at %p>",
+ PyString_AsString(func_name), (void *)op);
+#endif
+}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyCFunctionObject* f = (PyCFunctionObject*)func;
+ PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+ PyObject *self = PyCFunction_GET_SELF(func);
+ Py_ssize_t size;
+ switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ case METH_VARARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ return (*meth)(self, arg);
+ break;
+ case METH_VARARGS | METH_KEYWORDS:
+ return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+ case METH_NOARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 0)
+ return (*meth)(self, NULL);
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes no arguments (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ case METH_O:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 1)
+ return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes exactly one argument (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ default:
+ PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+ "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+ "longer supported!");
+ return NULL;
+ }
+ PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+ f->m_ml->ml_name);
+ return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ return PyCFunction_Call(func, arg, kw);
+}
+#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_CyFunction_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 !CYTHON_COMPILING_IN_PYPY
+ __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
+ if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+ return -1;
+ __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
+ return 0;
+}
+static CYTHON_INLINE 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 CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ m->defaults_tuple = tuple;
+ Py_INCREF(tuple);
+}
+
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;
"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 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_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#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;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-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
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
+ return NULL;
}
#endif
return NULL;
}
+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