/* Generated by Cython 0.16 on Tue Jan 15 06:50:15 2013 */ #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 /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #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 #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyCFunction_Call PyObject_Call #else #define __Pyx_PyCFunction_Call PyCFunction_Call #endif #if PY_VERSION_HEX < 0x02050000 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 PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) PyNumber_Int(o) #define PyIndex_Check(o) PyNumber_Check(o) #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #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_GET_LENGTH) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #else #define CYTHON_PEP393_ENABLED 0 #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #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_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) #define PyInt_FromString PyLong_FromString #define PyInt_FromUnicode PyLong_FromUnicode #define PyInt_FromLong PyLong_FromLong #define PyInt_FromSize_t PyLong_FromSize_t #define PyInt_FromSsize_t PyLong_FromSsize_t #define PyInt_AsLong PyLong_AsLong #define PyInt_AS_LONG PyLong_AS_LONG #define PyInt_AsSsize_t PyLong_AsSsize_t #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define 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_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #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)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #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) #else #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 #define __PYX_HAVE__pysam__cvcf #define __PYX_HAVE_API__pysam__cvcf #include "stdlib.h" #include "string.h" #include "stdint.h" #include "stdio.h" #include "ctype.h" #include "sys/types.h" #include "sys/stat.h" #include "fcntl.h" #include "unistd.h" #include "bgzf.h" #include "tabix.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif /* inline attribute */ #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ #elif defined(_MSC_VER) #define CYTHON_INLINE __inline #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else #define CYTHON_INLINE #endif #endif /* unused attribute */ #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif #endif typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ /* Type Conversion Predeclarations */ #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 Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; static const char *__pyx_f[] = { "cvcf.pyx", "ctabix.pxd", "TabProxies.pxd", }; /*--- Type declarations ---*/ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data; struct __pyx_obj_5pysam_10TabProxies_TupleProxy; struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy; struct __pyx_obj_5pysam_10TabProxies_BedProxy; struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator; struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed; struct __pyx_obj_5pysam_6ctabix_TabixIterator; struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse; struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator; struct __pyx_obj_5pysam_6ctabix_Parser; struct __pyx_obj_5pysam_4cvcf_asVCFRecord; struct __pyx_obj_5pysam_6ctabix_Tabixfile; struct __pyx_obj_5pysam_6ctabix_asBed; struct __pyx_obj_5pysam_6ctabix_asGTF; struct __pyx_obj_5pysam_10TabProxies_VCFProxy; struct __pyx_obj_5pysam_4cvcf_VCFRecord; struct __pyx_obj_5pysam_6ctabix_asTuple; struct __pyx_obj_5pysam_10TabProxies_GTFProxy; struct __pyx_obj_5pysam_6ctabix_asVCF; struct __pyx_defaults; typedef struct __pyx_defaults __pyx_defaults; struct __pyx_defaults1; typedef struct __pyx_defaults1 __pyx_defaults1; struct __pyx_defaults2; typedef struct __pyx_defaults2 __pyx_defaults2; struct __pyx_defaults3; typedef struct __pyx_defaults3 __pyx_defaults3; struct __pyx_defaults4; typedef struct __pyx_defaults4 __pyx_defaults4; struct __pyx_defaults { PyObject *__pyx_arg_leftalign; }; struct __pyx_defaults1 { PyObject *__pyx_arg_filter; }; struct __pyx_defaults2 { PyObject *__pyx_arg_filter; }; struct __pyx_defaults3 { PyObject *__pyx_arg_key; PyObject *__pyx_arg_value; }; struct __pyx_defaults4 { PyObject *__pyx_arg_lineparse; }; /* "pysam/cvcf.pyx":647 * return False * * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< * cols = line.split('\t') * if len(cols) != len(self._samples)+9: */ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data { PyObject_HEAD PyObject *__pyx_v_alt; }; /* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_TupleProxy { PyObject_HEAD struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab; char *data; char **fields; int nfields; int index; int nbytes; int offset; int is_modified; }; /* "TabProxies.pxd":69 * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; }; /* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_BedProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t start; uint32_t end; int bedfields; }; /* "ctabix.pxd":186 * cdef tabix_t * tabixfile * * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; /* "ctabix.pxd":205 * pass * * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "ctabix.pxd":182 * cdef char * _filename * * cdef class TabixIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; /* "ctabix.pxd":210 * cdef Parser parser * * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< * cdef FILE * infile * cdef char * buffer */ struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator { PyObject_HEAD struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab; FILE *infile; char *buffer; size_t size; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "pysam/cvcf.pyx":790 * if alt: * for i in range(1,min(len(ref),min(map(len,alt)))): * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< * break * ref, alt = ref[:-1], [allele[:-1] for allele in alt] */ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr { PyObject_HEAD struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope; PyObject *__pyx_v_allele; PyObject *__pyx_t_0; Py_ssize_t __pyx_t_1; PyObject *(*__pyx_t_2)(PyObject *); }; /* "pysam/cvcf.pyx":899 * return line * * def _parse(self, line, stream): # <<<<<<<<<<<<<< * # deal with files with header only * if line.startswith("##"): return */ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse { PyObject_HEAD PyObject *__pyx_v_d; PyObject *__pyx_v_line; PyObject *__pyx_v_self; PyObject *__pyx_v_stream; Py_ssize_t __pyx_t_0; PyObject *__pyx_t_1; PyObject *(*__pyx_t_2)(PyObject *); }; /* "ctabix.pxd":218 * cdef __cnext__(self) * * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< * cdef FILE * infile * cdef Parser parser */ struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator { PyObject_HEAD struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab; FILE *infile; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "ctabix.pxd":190 * cdef tabix_t * tabixfile * * cdef class Parser: # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_Parser { PyObject_HEAD }; /* "pysam/cvcf.pyx":226 * * * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a VCF record.''' * cdef vcffile */ struct __pyx_obj_5pysam_4cvcf_asVCFRecord { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; PyObject *vcffile; }; /* "ctabix.pxd":172 * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) * * cdef class Tabixfile: # <<<<<<<<<<<<<< * * # pointer to tabixfile */ struct __pyx_obj_5pysam_6ctabix_Tabixfile { PyObject_HEAD tabix_t *tabixfile; int isremote; char *_filename; }; /* "ctabix.pxd":199 * pass * * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asBed { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "ctabix.pxd":196 * pass * * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asGTF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_VCFProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t pos; }; /* "pysam/cvcf.pyx":94 * ########################################################################################################### * * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< * '''vcf record. * */ struct __pyx_obj_5pysam_4cvcf_VCFRecord { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; PyObject *vcf; char *contig; uint32_t pos; }; /* "ctabix.pxd":193 * pass * * cdef class asTuple(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asTuple { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_GTFProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; char *_attributes; int hasOwnAttributes; }; /* "ctabix.pxd":202 * pass * * cdef class asVCF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asVCF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy { int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t); PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); }; static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy; /* "TabProxies.pxd":69 * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; /* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy; /* "pysam/cvcf.pyx":94 * ########################################################################################################### * * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< * '''vcf record. * */ struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord; /* "ctabix.pxd":210 * cdef Parser parser * * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< * cdef FILE * infile * cdef char * buffer */ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator { PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *); }; static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator; /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *); }; static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy; /* "ctabix.pxd":218 * cdef __cnext__(self) * * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< * cdef FILE * infile * cdef Parser parser */ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator { PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *); }; static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator; /* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; 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if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { PyObject *r = PyList_GET_ITEM(o, n); Py_INCREF(r); return r; } } else if (PyTuple_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { PyObject *r = PyTuple_GET_ITEM(o, n); Py_INCREF(r); return r; } } else if (likely(i >= 0)) { PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_item)) { return m->sq_item(o, i); } } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*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 void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ #define __Pyx_PyObject_AsDouble(obj) \ ((likely(PyFloat_CheckExact(obj))) ? \ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void); #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; if (unlikely(d == Py_None)) { __Pyx_RaiseNoneIndexingError(); return NULL; } value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) PyErr_SetObject(PyExc_KeyError, key); return NULL; } Py_INCREF(value); return value; } #else #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) { return unlikely(b < 0) ? b : !b; } static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { if (PyList_Append(L, x) < 0) return NULL; Py_INCREF(Py_None); return Py_None; /* this is just to have an accurate signature */ } else { PyObject *r, *m; m = __Pyx_GetAttrString(L, "append"); if (!m) return NULL; r = PyObject_CallFunctionObjArgs(m, x, NULL); Py_DECREF(m); return r; } } #define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_SetItemInt_Fast(o, i, v) : \ __Pyx_SetItemInt_Generic(o, to_py_func(i), v)) static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { int r; 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if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char *)"discard", (char *)"O", key); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char *)"add", (char *)"O", key); if (!ret) return -1; Py_DECREF(ret); return 0; } #endif /* PyAnySet_CheckExact (<= Py2.4) */ #endif /* < Py2.5 */ 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, long level); /*proto*/ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name); 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 #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; 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/*proto*/ #define __Pyx_Generator_USED #include typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); typedef struct { PyObject_HEAD __pyx_generator_body_t body; PyObject *closure; int is_running; int resume_label; PyObject *exc_type; PyObject *exc_value; PyObject *exc_traceback; PyObject *gi_weakreflist; PyObject *classobj; } __pyx_GeneratorObject; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure); static int __pyx_Generator_init(void); static int __Pyx_check_binary_version(void); #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'pysam' */ /* Module declarations from 'pysam.ctabix' */ static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0; /* Module declarations from 'pysam.TabProxies' */ static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0; /* Module declarations from 'pysam.cvcf' */ static PyTypeObject *__pyx_ptype_5pysam_4cvcf_VCFRecord = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf_asVCFRecord = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = 0; #define __Pyx_MODULE_NAME "pysam.cvcf" int __pyx_module_is_main_pysam__cvcf = 0; /* Implementation of 'pysam.cvcf' */ static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_min; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */ static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ static Py_ssize_t __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static int __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */ static char __pyx_k_1[] = ""; static char __pyx_k_2[] = ","; static char __pyx_k_4[] = ":"; static char __pyx_k_6[] = "-"; static char __pyx_k_8[] = "Don't understand region string '%s'"; static char __pyx_k_9[] = "."; static char __pyx_k_11[] = ";"; static char __pyx_k_14[] = "="; static char __pyx_k_18[] = "BAD_NUMBER_OF_VALUES"; static char __pyx_k_19[] = "(found %s values in element %s; expected %s)"; static char __pyx_k_20[] = "BAD_NUMBER_OF_PARAMETERS"; static char __pyx_k_21[] = "id=%s, expected %s parameters, got %s"; static char __pyx_k_24[] = " in line %s: '%s'\n%s %s: %s\n"; static char __pyx_k_25[] = "<"; static char __pyx_k_27[] = "V40_MISSING_ANGLE_BRACKETS"; static char __pyx_k_28[] = ">"; static char __pyx_k_32[] = "\""; static char __pyx_k_36[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS"; static char __pyx_k_37[] = "BADLY_FORMATTED_FORMAT_STRING"; static char __pyx_k_38[] = "ID="; static char __pyx_k_39[] = "Number="; static char __pyx_k_40[] = "Type="; static char __pyx_k_41[] = "Description="; static char __pyx_k_50[] = "FORMAT_MISSING_QUOTES"; static char __pyx_k_53[] = "#alleles"; static char __pyx_k_54[] = "#nonref_alleles"; static char __pyx_k_55[] = "#genotypes"; static char __pyx_k_56[] = "#phased_genotypes"; static char __pyx_k_57[] = "ZERO_FOR_NON_FLAG_FIELD"; static char __pyx_k_58[] = "Unknown number type encountered: %s"; static char __pyx_k_59[] = "%s=%s"; static char __pyx_k_60[] = "(Undefined tag)"; static char __pyx_k_61[] = "(output)"; static char __pyx_k_64[] = "Read depth at this position for this sample"; static char __pyx_k_65[] = "Sample Genotype Filter"; static char __pyx_k_66[] = "Genotype likelihoods"; static char __pyx_k_67[] = "Genotype Quality"; static char __pyx_k_68[] = "Phred-scaled genotype likelihoods"; static char __pyx_k_69[] = "Genotype posterior probabilities"; static char __pyx_k_70[] = "Conditional genotype quality"; static char __pyx_k_71[] = "Haplotype Quality"; static char __pyx_k_72[] = "Phase set"; static char __pyx_k_73[] = "Phasing quality"; static char __pyx_k_74[] = "Expected alternate allel counts"; static char __pyx_k_75[] = "RMS mapping quality"; static char __pyx_k_76[] = "##"; static char __pyx_k_79[] = "VCFv3.3"; static char __pyx_k_80[] = "VCFv4.0"; static char __pyx_k_81[] = "VCFv4.1"; static char __pyx_k_82[] = "UNKNOWN_FORMAT_STRING"; static char __pyx_k_83[] = "##fileformat=VCFv%s.%s\n"; static char __pyx_k_84[] = "##%s=%s\n"; static char __pyx_k_85[] = "#"; static char __pyx_k_88[] = "\t"; static char __pyx_k_90[] = "HEADING_NOT_SEPARATED_BY_TABS"; static char __pyx_k_91[] = "(%sth entry not found)"; static char __pyx_k_92[] = "(found %s, expected %s)"; static char __pyx_k_93[] = "BADLY_FORMATTED_HEADING"; static char __pyx_k_94[] = "\n"; static char __pyx_k_95[] = "|"; static char __pyx_k_96[] = "ERROR_FLAG_HAS_VALUE"; static char __pyx_k__0[] = "0"; static char __pyx_k__A[] = "A"; static char __pyx_k__D[] = "D"; static char __pyx_k__G[] = "G"; static char __pyx_k__I[] = "I"; static char __pyx_k__N[] = "N"; static char __pyx_k__a[] = "a"; static char __pyx_k__c[] = "c"; static char __pyx_k__d[] = "d"; static char __pyx_k__f[] = "f"; static char __pyx_k__i[] = "i"; static char __pyx_k__k[] = "k"; static char __pyx_k__l[] = "l"; static char __pyx_k__n[] = "n"; static char __pyx_k__r[] = "r"; static char __pyx_k__s[] = "s"; static char __pyx_k__t[] = "t"; static char __pyx_k__v[] = "v"; static char __pyx_k__x[] = "x"; static char __pyx_k__y[] = "y"; static char __pyx_k_100[] = "ERROR_FORMAT_NOT_INTEGER"; static char __pyx_k_101[] = "ERROR_FORMAT_NOT_CHAR"; static char __pyx_k_102[] = "ERROR_FORMAT_NOT_NUMERICAL"; static char __pyx_k_104[] = "BAD_NUMBER_OF_COLUMNS"; static char __pyx_k_105[] = "expected %s for %s samples (%s), got %s"; static char __pyx_k_106[] = "(reference is %s, VCF says %s)"; static char __pyx_k_114[] = "V33_UNMATCHED_DELETION"; static char __pyx_k_115[] = "(deletion is %s, reference is %s)"; static char __pyx_k_116[] = "MISSING_INDEL_ALLELE_REF_BASE"; static char __pyx_k_118[] = "Required key %s not found in data"; static char __pyx_k_121[] = "enter_default_format"; static char __pyx_k_123[] = "Can only handle v3.3 and v4.0 VCF files"; static char __pyx_k_125[] = "Invalid error string: %s"; static char __pyx_k_126[] = "needs to be checked"; static char __pyx_k_128[] = "[|/\\\\]"; static char __pyx_k_130[] = "^[ACGTN]+$"; static char __pyx_k_134[] = "/home/andreas/devel/pysam/pysam/cvcf.pyx"; static char __pyx_k_135[] = "pysam.cvcf"; static char __pyx_k_138[] = "id numbertype number type description missingvalue"; static char __pyx_k_140[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; static char __pyx_k_141[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; static char __pyx_k_142[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s"; static char __pyx_k_143[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)"; static char __pyx_k_144[] = "POS_NOT_NUMERICAL:Position column is not numerical"; static char __pyx_k_145[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field"; static char __pyx_k_146[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF"; static char __pyx_k_147[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF"; static char __pyx_k_148[] = "POS_NOT_POSITIVE:Position field must be >0"; static char __pyx_k_149[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'"; static char __pyx_k_150[] = "ERROR_INFO_STRING:Error while parsing info field"; static char __pyx_k_151[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)"; static char __pyx_k_152[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s"; static char __pyx_k_153[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string"; static char __pyx_k_154[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header"; static char __pyx_k_155[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header"; static char __pyx_k_156[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)"; static char __pyx_k_157[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)"; static char __pyx_k_158[] = "BAD_GENOTYPE:Cannot parse genotype (%s)"; static char __pyx_k_159[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)"; static char __pyx_k_160[] = "MISSING_REF:Reference allele missing"; static char __pyx_k_161[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)"; static char __pyx_k_162[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets"; static char __pyx_k_163[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes"; static char __pyx_k_164[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields"; static char __pyx_k_165[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs"; static char __pyx_k_166[] = "WRONG_REF:Wrong reference %s"; static char __pyx_k_167[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data"; static char __pyx_k_168[] = "BAD_CHR_TAG:Error calculating chr tag for %s"; static char __pyx_k_169[] = "ZERO_LENGTH_ALLELE:Found zero-length allele"; static char __pyx_k_170[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"; static char __pyx_k_171[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'"; static char __pyx_k_172[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s"; static char __pyx_k_173[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value"; static char __pyx_k__DP[] = "DP"; static char __pyx_k__EC[] = "EC"; static char __pyx_k__FT[] = "FT"; static char __pyx_k__GL[] = "GL"; static char __pyx_k__GP[] = "GP"; static char __pyx_k__GQ[] = "GQ"; static char __pyx_k__GT[] = "GT"; static char __pyx_k__HQ[] = "HQ"; static char __pyx_k__ID[] = "ID"; static char __pyx_k__MQ[] = "MQ"; static char __pyx_k__PL[] = "PL"; static char __pyx_k__PQ[] = "PQ"; static char __pyx_k__PS[] = "PS"; static char __pyx_k__fa[] = "fa"; static char __pyx_k__id[] = "id"; static char __pyx_k__na[] = "na"; static char __pyx_k__re[] = "re"; static char __pyx_k__ALT[] = "ALT"; static char __pyx_k__GLE[] = "GLE"; static char __pyx_k__POS[] = "POS"; static char __pyx_k__REF[] = "REF"; static char __pyx_k__VCF[] = "VCF"; static char __pyx_k__add[] = "add"; static char __pyx_k__alt[] = "alt"; static char __pyx_k__end[] = "end"; static char __pyx_k__err[] = "err"; static char __pyx_k__fmt[] = "fmt"; static char __pyx_k__get[] = "get"; static char __pyx_k__gts[] = "gts"; static char __pyx_k__idx[] = "idx"; static char __pyx_k__key[] = "key"; static char __pyx_k__len[] = "len"; static char __pyx_k__map[] = "map"; static char __pyx_k__min[] = "min"; static char __pyx_k__nmb[] = "nmb"; static char __pyx_k__opt[] = "opt"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__ref[] = "ref"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__var[] = "var"; static char __pyx_k__vcf[] = "vcf"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__Flag[] = "Flag"; static char __pyx_k__INFO[] = "INFO"; static char __pyx_k__PASS[] = "PASS"; static char __pyx_k__QUAL[] = "QUAL"; static char __pyx_k__Type[] = "Type"; static char __pyx_k__addn[] = "addn"; static char __pyx_k__alt1[] = "alt1"; static char __pyx_k__alt2[] = "alt2"; static char __pyx_k__cols[] = "cols"; static char __pyx_k__copy[] = "copy"; static char __pyx_k__data[] = "data"; static char __pyx_k__dict[] = "dict"; static char __pyx_k__elts[] = "elts"; static char __pyx_k__find[] = "find"; static char __pyx_k__info[] = "info"; static char __pyx_k__join[] = "join"; static char __pyx_k__keys[] = "keys"; static char __pyx_k__last[] = "last"; static char __pyx_k__left[] = "left"; static char __pyx_k__line[] = "line"; static char __pyx_k__pos1[] = "pos1"; static char __pyx_k__pos2[] = "pos2"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__ref1[] = "ref1"; static char __pyx_k__ref2[] = "ref2"; static char __pyx_k__rest[] = "rest"; static char __pyx_k__self[] = "self"; static char __pyx_k__type[] = "type"; static char __pyx_k__ACGTN[] = "ACGTN"; static char __pyx_k__CHROM[] = "CHROM"; static char __pyx_k__Error[] = "Error"; static char __pyx_k__Float[] = "Float"; static char __pyx_k___copy[] = "_copy"; static char __pyx_k___info[] = "_info"; static char __pyx_k___line[] = "_line"; static char __pyx_k__addns[] = "addns"; static char __pyx_k__blurp[] = "blurp"; static char __pyx_k__chrom[] = "chrom"; static char __pyx_k__descr[] = "descr"; static char __pyx_k__error[] = "error"; static char __pyx_k__faref[] = "faref"; static char __pyx_k__fetch[] = "fetch"; static char __pyx_k__first[] = "first"; static char __pyx_k__ielts[] = "ielts"; static char __pyx_k__label[] = "label"; static char __pyx_k__lines[] = "lines"; static char __pyx_k__match[] = "match"; static char __pyx_k__parse[] = "parse"; static char __pyx_k__pysam[] = "pysam"; static char __pyx_k__range[] = "range"; static char __pyx_k__sdata[] = "sdata"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; static char __pyx_k__upper[] = "upper"; static char __pyx_k__value[] = "value"; static char __pyx_k__write[] = "write"; static char __pyx_k__FILTER[] = "FILTER"; static char __pyx_k__FORMAT[] = "FORMAT"; static char __pyx_k__GTdata[] = "GTdata"; static char __pyx_k__Number[] = "Number"; static char __pyx_k__String[] = "String"; static char __pyx_k___lines[] = "_lines"; static char __pyx_k___parse[] = "_parse"; static char __pyx_k__allele[] = "allele"; static char __pyx_k__bisect[] = "bisect"; static char __pyx_k__buffer[] = "buffer"; static char __pyx_k__filter[] = "filter"; static char __pyx_k__format[] = "format"; static char __pyx_k__header[] = "header"; static char __pyx_k__number[] = "number"; static char __pyx_k__object[] = "object"; static char __pyx_k__output[] = "output"; static char __pyx_k__parser[] = "parser"; static char __pyx_k__record[] = "record"; static char __pyx_k__region[] = "region"; static char __pyx_k__result[] = "result"; static char __pyx_k__sample[] = "sample"; static char __pyx_k__stream[] = "stream"; static char __pyx_k__string[] = "string"; static char __pyx_k__values[] = "values"; static char __pyx_k__Integer[] = "Integer"; static char __pyx_k__Warning[] = "Warning"; static char __pyx_k____all__[] = "__all__"; static char __pyx_k___errors[] = "_errors"; static char __pyx_k___filter[] = "_filter"; static char __pyx_k___format[] = "_format"; static char __pyx_k___header[] = "_header"; static char __pyx_k___lineno[] = "_lineno"; static char __pyx_k__compile[] = "compile"; static char __pyx_k__connect[] = "connect"; static char __pyx_k__errwarn[] = "errwarn"; static char __pyx_k__genexpr[] = "genexpr"; static char __pyx_k__getinfo[] = "getinfo"; static char __pyx_k__longest[] = "longest"; static char __pyx_k__missing[] = "missing"; static char __pyx_k__movable[] = "movable"; static char __pyx_k__newalts[] = "newalts"; static char __pyx_k__regions[] = "regions"; static char __pyx_k__replace[] = "replace"; static char __pyx_k__samples[] = "samples"; static char __pyx_k__setinfo[] = "setinfo"; static char __pyx_k__vcffile[] = "vcffile"; static char __pyx_k__version[] = "version"; static char __pyx_k__GTstring[] = "GTstring"; static char __pyx_k__Genotype[] = "Genotype"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k____dict__[] = "__dict__"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k___regions[] = "_regions"; static char __pyx_k___samples[] = "_samples"; static char __pyx_k___version[] = "_version"; static char __pyx_k__deepcopy[] = "deepcopy"; static char __pyx_k__endswith[] = "endswith"; static char __pyx_k__expected[] = "expected"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__gtsRegEx[] = "gtsRegEx"; static char __pyx_k__headings[] = "headings"; static char __pyx_k__inregion[] = "inregion"; static char __pyx_k__operator[] = "operator"; static char __pyx_k__required[] = "required"; static char __pyx_k__sequence[] = "sequence"; static char __pyx_k__shortest[] = "shortest"; static char __pyx_k__validate[] = "validate"; static char __pyx_k__Character[] = "Character"; static char __pyx_k__NT_NUMBER[] = "NT_NUMBER"; static char __pyx_k__Tabixfile[] = "Tabixfile"; static char __pyx_k__VCFRecord[] = "VCFRecord"; static char __pyx_k__WRONG_REF[] = "WRONG_REF"; static char __pyx_k___required[] = "_required"; static char __pyx_k__convertGT[] = "convertGT"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__getfilter[] = "getfilter"; static char __pyx_k__getformat[] = "getformat"; static char __pyx_k__getheader[] = "getheader"; static char __pyx_k__last_line[] = "last_line"; static char __pyx_k__leftalign[] = "leftalign"; static char __pyx_k__lineparse[] = "lineparse"; static char __pyx_k__reference[] = "reference"; static char __pyx_k__separator[] = "separator"; static char __pyx_k__setfilter[] = "setfilter"; static char __pyx_k__setformat[] = "setformat"; static char __pyx_k__setheader[] = "setheader"; static char __pyx_k__tabixfile[] = "tabixfile"; static char __pyx_k__warnerror[] = "warnerror"; static char __pyx_k__NT_ALLELES[] = "NT_ALLELES"; static char __pyx_k__NT_UNKNOWN[] = "NT_UNKNOWN"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k___leftalign[] = "_leftalign"; static char __pyx_k___reference[] = "_reference"; static char __pyx_k__errorlabel[] = "errorlabel"; static char __pyx_k__fileformat[] = "fileformat"; static char __pyx_k__formatdict[] = "formatdict"; static char __pyx_k__getsamples[] = "getsamples"; static char __pyx_k__itemgetter[] = "itemgetter"; static char __pyx_k__itervalues[] = "itervalues"; static char __pyx_k__namedtuple[] = "namedtuple"; static char __pyx_k__numbertype[] = "numbertype"; static char __pyx_k__parse_data[] = "parse_data"; static char __pyx_k__setregions[] = "setregions"; static char __pyx_k__setsamples[] = "setsamples"; static char __pyx_k__setversion[] = "setversion"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__write_data[] = "write_data"; static char __pyx_k__Description[] = "Description"; static char __pyx_k__MISSING_REF[] = "MISSING_REF"; static char __pyx_k__V33_BAD_REF[] = "V33_BAD_REF"; static char __pyx_k__alleleRegEx[] = "alleleRegEx"; static char __pyx_k__collections[] = "collections"; static char __pyx_k__defaultdict[] = "defaultdict"; static char __pyx_k__description[] = "description"; static char __pyx_k__errorstring[] = "errorstring"; static char __pyx_k__ignoreerror[] = "ignoreerror"; static char __pyx_k__writeheader[] = "writeheader"; static char __pyx_k__BAD_GENOTYPE[] = "BAD_GENOTYPE"; static char __pyx_k__NT_GENOTYPES[] = "NT_GENOTYPES"; static char __pyx_k___warn_errors[] = "_warn_errors"; static char __pyx_k__get_expected[] = "get_expected"; static char __pyx_k__get_sequence[] = "get_sequence"; static char __pyx_k__missingvalue[] = "missingvalue"; static char __pyx_k__parse_format[] = "parse_format"; static char __pyx_k__parse_header[] = "parse_header"; static char __pyx_k__setreference[] = "setreference"; static char __pyx_k__write_header[] = "write_header"; static char __pyx_k__NT_NR_ALLELES[] = "NT_NR_ALLELES"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k___parse_header[] = "_parse_header"; static char __pyx_k__compare_calls[] = "compare_calls"; static char __pyx_k__convertGTback[] = "convertGTback"; static char __pyx_k__datagenerator[] = "datagenerator"; static char __pyx_k__format_format[] = "format_format"; static char __pyx_k__parse_heading[] = "parse_heading"; static char __pyx_k__parse_regions[] = "parse_regions"; static char __pyx_k__write_heading[] = "write_heading"; static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE"; static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE"; static char __pyx_k___sample2column[] = "_sample2column"; static char __pyx_k__have_deletions[] = "have_deletions"; static char __pyx_k___add_definition[] = "_add_definition"; static char __pyx_k___ignored_errors[] = "_ignored_errors"; static char __pyx_k__faref_leftflank[] = "faref_leftflank"; static char __pyx_k__POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE"; static char __pyx_k__parse_formatdata[] = "parse_formatdata"; static char __pyx_k__ERROR_INFO_STRING[] = "ERROR_INFO_STRING"; static char __pyx_k__ERROR_UNKNOWN_KEY[] = "ERROR_UNKNOWN_KEY"; static char __pyx_k__POS_NOT_NUMERICAL[] = "POS_NOT_NUMERICAL"; static char __pyx_k__format_formatdata[] = "format_formatdata"; static char __pyx_k__FILTER_NOT_DEFINED[] = "FILTER_NOT_DEFINED"; static char __pyx_k__FORMAT_NOT_DEFINED[] = "FORMAT_NOT_DEFINED"; static char __pyx_k__QUAL_NOT_NUMERICAL[] = "QUAL_NOT_NUMERICAL"; static char __pyx_k__ZERO_LENGTH_ALLELE[] = "ZERO_LENGTH_ALLELE"; static char __pyx_k__ERROR_TRAILING_DATA[] = "ERROR_TRAILING_DATA"; static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF"; static PyObject *__pyx_kp_s_1; 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static PyObject *__pyx_kp_s_150; static PyObject *__pyx_kp_s_151; static PyObject *__pyx_kp_s_152; static PyObject *__pyx_kp_s_153; static PyObject *__pyx_kp_s_154; static PyObject *__pyx_kp_s_155; static PyObject *__pyx_kp_s_156; static PyObject *__pyx_kp_s_157; static PyObject *__pyx_kp_s_158; static PyObject *__pyx_kp_s_159; static PyObject *__pyx_kp_s_160; static PyObject *__pyx_kp_s_161; static PyObject *__pyx_kp_s_162; static PyObject *__pyx_kp_s_163; static PyObject *__pyx_kp_s_164; static PyObject *__pyx_kp_s_165; static PyObject *__pyx_kp_s_166; static PyObject *__pyx_kp_s_167; static PyObject *__pyx_kp_s_168; static PyObject *__pyx_kp_s_169; static PyObject *__pyx_kp_s_170; static PyObject *__pyx_kp_s_171; static PyObject *__pyx_kp_s_172; static PyObject *__pyx_kp_s_173; static PyObject *__pyx_n_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_2; static PyObject *__pyx_n_s_20; static PyObject *__pyx_kp_s_21; static PyObject *__pyx_kp_s_24; static PyObject *__pyx_kp_s_25; static PyObject *__pyx_n_s_27; static PyObject *__pyx_kp_s_28; static PyObject *__pyx_kp_s_32; static PyObject *__pyx_n_s_36; static PyObject *__pyx_n_s_37; static PyObject *__pyx_kp_s_38; static PyObject *__pyx_kp_s_39; static PyObject *__pyx_kp_s_4; static PyObject *__pyx_kp_s_40; static PyObject *__pyx_kp_s_41; static PyObject *__pyx_n_s_50; static PyObject *__pyx_kp_s_53; static PyObject *__pyx_kp_s_54; static PyObject *__pyx_kp_s_55; static PyObject *__pyx_kp_s_56; static PyObject *__pyx_n_s_57; static PyObject *__pyx_kp_s_58; static PyObject *__pyx_kp_s_59; static PyObject *__pyx_kp_s_6; static PyObject *__pyx_kp_s_60; static PyObject *__pyx_kp_s_61; static PyObject *__pyx_kp_s_64; static PyObject *__pyx_kp_s_65; static PyObject *__pyx_kp_s_66; static PyObject *__pyx_kp_s_67; static PyObject *__pyx_kp_s_68; static PyObject *__pyx_kp_s_69; static PyObject *__pyx_kp_s_70; static PyObject *__pyx_kp_s_71; static PyObject *__pyx_kp_s_72; static PyObject *__pyx_kp_s_73; static PyObject *__pyx_kp_s_74; static PyObject *__pyx_kp_s_75; static PyObject *__pyx_kp_s_76; static PyObject *__pyx_kp_s_79; static PyObject *__pyx_kp_s_8; static PyObject *__pyx_kp_s_80; static PyObject *__pyx_kp_s_81; static PyObject *__pyx_n_s_82; static PyObject *__pyx_kp_s_83; static PyObject *__pyx_kp_s_84; static PyObject *__pyx_kp_s_85; static PyObject *__pyx_kp_s_88; static PyObject *__pyx_kp_b_9; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_n_s_90; static PyObject *__pyx_kp_s_91; static PyObject *__pyx_kp_s_92; static PyObject *__pyx_n_s_93; static PyObject *__pyx_kp_s_94; static PyObject *__pyx_kp_s_95; static PyObject *__pyx_n_s_96; static PyObject *__pyx_kp_b__0; static PyObject *__pyx_kp_s__0; static PyObject *__pyx_n_s__A; static PyObject *__pyx_n_s__ACGTN; static PyObject *__pyx_n_s__ALT; static PyObject *__pyx_n_s__BAD_GENOTYPE; static PyObject *__pyx_n_s__CHROM; static PyObject *__pyx_n_s__Character; static PyObject *__pyx_n_s__D; static PyObject *__pyx_n_s__DP; static PyObject *__pyx_n_s__Description; static PyObject *__pyx_n_s__EC; static PyObject *__pyx_n_s__ERROR_INFO_STRING; static PyObject *__pyx_n_s__ERROR_TRAILING_DATA; static PyObject *__pyx_n_s__ERROR_UNKNOWN_KEY; static PyObject *__pyx_n_s__Error; static PyObject *__pyx_n_s__FILTER; static PyObject *__pyx_n_s__FILTER_NOT_DEFINED; static PyObject *__pyx_n_s__FORMAT; static PyObject *__pyx_n_s__FORMAT_NOT_DEFINED; static PyObject *__pyx_n_s__FT; static PyObject *__pyx_n_s__Flag; static PyObject *__pyx_n_s__Float; static PyObject *__pyx_n_s__G; static PyObject *__pyx_n_s__GL; static PyObject *__pyx_n_s__GLE; static PyObject *__pyx_n_s__GP; static PyObject *__pyx_n_s__GQ; static PyObject *__pyx_n_s__GT; static PyObject *__pyx_n_s__GTdata; static PyObject *__pyx_n_s__GTstring; static PyObject *__pyx_n_s__Genotype; static PyObject *__pyx_n_s__HQ; static PyObject *__pyx_n_s__I; static PyObject *__pyx_n_s__ID; static PyObject *__pyx_n_s__INFO; static PyObject *__pyx_n_s__Integer; static PyObject *__pyx_n_s__KeyError; static PyObject *__pyx_n_s__MISSING_REF; static PyObject *__pyx_n_s__MQ; static PyObject *__pyx_n_s__N; static PyObject *__pyx_n_s__NT_ALLELES; static PyObject *__pyx_n_s__NT_GENOTYPES; static PyObject *__pyx_n_s__NT_NR_ALLELES; static PyObject *__pyx_n_s__NT_NUMBER; static PyObject *__pyx_n_s__NT_PHASED_GENOTYPES; static PyObject *__pyx_n_s__NT_UNKNOWN; static PyObject *__pyx_n_s__NotImplementedError; static PyObject *__pyx_n_s__Number; static PyObject *__pyx_n_b__PASS; static PyObject *__pyx_n_s__PASS; static PyObject *__pyx_n_s__PL; static PyObject *__pyx_n_s__POS; static PyObject *__pyx_n_s__POS_NOT_NUMERICAL; static PyObject *__pyx_n_s__POS_NOT_POSITIVE; static PyObject *__pyx_n_s__PQ; static PyObject *__pyx_n_s__PS; static PyObject *__pyx_n_s__QUAL; static PyObject *__pyx_n_s__QUAL_NOT_NUMERICAL; static PyObject *__pyx_n_s__REF; static PyObject *__pyx_n_s__StopIteration; static PyObject *__pyx_n_s__String; static PyObject *__pyx_n_s__Tabixfile; static PyObject *__pyx_n_s__Type; static PyObject *__pyx_n_s__UNKNOWN_CHAR_IN_REF; static PyObject *__pyx_n_s__V33_BAD_ALLELE; static PyObject *__pyx_n_s__V33_BAD_REF; static PyObject *__pyx_n_s__V40_BAD_ALLELE; static PyObject *__pyx_n_s__VCF; static PyObject *__pyx_n_s__VCFRecord; static PyObject *__pyx_n_s__ValueError; static PyObject *__pyx_n_s__WRONG_REF; static PyObject *__pyx_n_s__Warning; static PyObject *__pyx_n_s__ZERO_LENGTH_ALLELE; static PyObject *__pyx_n_s____all__; static PyObject *__pyx_n_s____dict__; static PyObject *__pyx_n_s____init__; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s___add_definition; static PyObject *__pyx_n_s___copy; static PyObject *__pyx_n_s___errors; static PyObject *__pyx_n_s___filter; static PyObject *__pyx_n_s___format; static PyObject *__pyx_n_s___header; static PyObject *__pyx_n_s___ignored_errors; static PyObject *__pyx_n_s___info; static PyObject *__pyx_n_s___leftalign; static PyObject *__pyx_n_s___line; static PyObject *__pyx_n_s___lineno; static PyObject *__pyx_n_s___lines; static PyObject *__pyx_n_s___parse; static PyObject *__pyx_n_s___parse_header; static PyObject *__pyx_n_s___reference; static PyObject *__pyx_n_s___regions; static PyObject *__pyx_n_s___required; static PyObject *__pyx_n_s___sample2column; static PyObject *__pyx_n_s___samples; static PyObject *__pyx_n_s___version; static PyObject *__pyx_n_s___warn_errors; static PyObject *__pyx_n_s__a; static PyObject *__pyx_n_s__add; static PyObject *__pyx_n_s__addn; static PyObject *__pyx_n_s__addns; static PyObject *__pyx_n_s__allele; static PyObject *__pyx_n_s__alleleRegEx; static PyObject *__pyx_n_s__alt; static PyObject *__pyx_n_s__alt1; static PyObject *__pyx_n_s__alt2; static PyObject *__pyx_n_s__bisect; static PyObject *__pyx_n_s__blurp; static PyObject *__pyx_n_s__buffer; static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__chrom; static PyObject *__pyx_n_s__collections; static PyObject *__pyx_n_s__cols; static PyObject *__pyx_n_s__compare_calls; static PyObject *__pyx_n_s__compile; static PyObject *__pyx_n_s__connect; static PyObject *__pyx_n_s__convertGT; static PyObject *__pyx_n_s__convertGTback; static PyObject *__pyx_n_s__copy; static PyObject *__pyx_n_s__d; static PyObject *__pyx_n_s__data; static PyObject *__pyx_n_s__datagenerator; static PyObject *__pyx_n_s__deepcopy; static PyObject *__pyx_n_s__defaultdict; static PyObject *__pyx_n_s__descr; static PyObject *__pyx_n_s__description; static PyObject *__pyx_n_s__dict; static PyObject *__pyx_n_s__elts; static PyObject *__pyx_n_s__end; static PyObject *__pyx_n_s__endswith; static PyObject *__pyx_n_s__enumerate; static PyObject *__pyx_n_s__err; static PyObject *__pyx_n_s__error; static PyObject *__pyx_n_s__errorlabel; static PyObject *__pyx_n_s__errorstring; static PyObject *__pyx_n_s__errwarn; static PyObject *__pyx_n_s__expected; static PyObject *__pyx_n_s__f; static PyObject *__pyx_n_s__fa; static PyObject *__pyx_n_s__faref; static PyObject *__pyx_n_s__faref_leftflank; static PyObject *__pyx_n_s__fetch; static PyObject *__pyx_n_s__fileformat; static PyObject *__pyx_n_s__filename; static PyObject *__pyx_n_s__filter; static PyObject *__pyx_n_s__find; static PyObject *__pyx_n_s__first; static PyObject *__pyx_n_s__fmt; static PyObject *__pyx_n_s__format; static PyObject *__pyx_n_s__format_format; static PyObject *__pyx_n_s__format_formatdata; static PyObject *__pyx_n_s__formatdict; static PyObject *__pyx_n_s__genexpr; static PyObject *__pyx_n_s__get; static PyObject *__pyx_n_s__get_expected; static PyObject *__pyx_n_s__get_sequence; static PyObject *__pyx_n_s__getfilter; static PyObject *__pyx_n_s__getformat; static PyObject *__pyx_n_s__getheader; static PyObject *__pyx_n_s__getinfo; static PyObject *__pyx_n_s__getsamples; static PyObject *__pyx_n_s__gts; static PyObject *__pyx_n_s__gtsRegEx; static PyObject *__pyx_n_s__have_deletions; static PyObject *__pyx_n_s__header; static PyObject *__pyx_n_s__headings; static PyObject *__pyx_n_s__i; static PyObject *__pyx_n_s__id; static PyObject *__pyx_n_s__idx; static PyObject *__pyx_n_s__ielts; static PyObject *__pyx_n_s__ignoreerror; static PyObject *__pyx_n_s__info; static PyObject *__pyx_n_s__inregion; static PyObject *__pyx_n_s__itemgetter; static PyObject *__pyx_n_s__itervalues; static PyObject *__pyx_n_s__join; static PyObject *__pyx_n_s__k; static PyObject *__pyx_n_s__key; static PyObject *__pyx_n_s__keys; static PyObject *__pyx_n_s__l; static PyObject *__pyx_n_s__label; static PyObject *__pyx_n_s__last; static PyObject *__pyx_n_s__last_line; static PyObject *__pyx_n_s__left; static PyObject *__pyx_n_s__leftalign; static PyObject *__pyx_n_s__len; static PyObject *__pyx_n_s__line; static PyObject *__pyx_n_s__lineparse; static PyObject *__pyx_n_s__lines; static PyObject *__pyx_n_s__longest; static PyObject *__pyx_n_s__map; static PyObject *__pyx_n_s__match; static PyObject *__pyx_n_s__min; static PyObject *__pyx_n_s__missing; static PyObject *__pyx_n_s__missingvalue; static PyObject *__pyx_n_s__movable; static PyObject *__pyx_n_s__n; static PyObject *__pyx_n_s__na; static PyObject *__pyx_n_s__namedtuple; static PyObject *__pyx_n_s__newalts; static PyObject *__pyx_n_s__nmb; static PyObject *__pyx_n_s__number; static PyObject *__pyx_n_s__numbertype; static PyObject *__pyx_n_s__object; static PyObject *__pyx_n_s__operator; static PyObject *__pyx_n_s__opt; static PyObject *__pyx_n_s__output; static PyObject *__pyx_n_s__parse; static PyObject *__pyx_n_s__parse_data; static PyObject *__pyx_n_s__parse_format; static PyObject *__pyx_n_s__parse_formatdata; static PyObject *__pyx_n_s__parse_header; static PyObject *__pyx_n_s__parse_heading; static PyObject *__pyx_n_s__parse_regions; static PyObject *__pyx_n_s__parser; static PyObject *__pyx_n_s__pos; static PyObject *__pyx_n_s__pos1; static PyObject *__pyx_n_s__pos2; static PyObject *__pyx_n_s__pysam; static PyObject *__pyx_n_s__qual; static PyObject *__pyx_n_s__r; static PyObject *__pyx_n_s__range; static PyObject *__pyx_n_s__re; static PyObject *__pyx_n_s__record; static PyObject *__pyx_n_s__ref; static PyObject *__pyx_n_s__ref1; static PyObject *__pyx_n_s__ref2; static PyObject *__pyx_n_s__reference; static PyObject *__pyx_n_s__region; static PyObject *__pyx_n_s__regions; static PyObject *__pyx_n_s__replace; static PyObject *__pyx_n_s__required; static PyObject *__pyx_n_s__rest; static PyObject *__pyx_n_s__result; static PyObject *__pyx_n_s__s; static PyObject *__pyx_n_s__sample; static PyObject *__pyx_n_s__samples; static PyObject *__pyx_n_s__sdata; static PyObject *__pyx_n_s__self; static PyObject *__pyx_n_s__separator; static PyObject *__pyx_n_s__sequence; static PyObject *__pyx_n_s__setfilter; static PyObject *__pyx_n_s__setformat; static PyObject *__pyx_n_s__setheader; static PyObject *__pyx_n_s__setinfo; static PyObject *__pyx_n_s__setreference; static PyObject *__pyx_n_s__setregions; static PyObject *__pyx_n_s__setsamples; static PyObject *__pyx_n_s__setversion; static PyObject *__pyx_n_s__shortest; static PyObject *__pyx_n_s__split; static PyObject *__pyx_n_s__start; static PyObject *__pyx_n_s__startswith; static PyObject *__pyx_n_s__stream; static PyObject *__pyx_n_s__string; static PyObject *__pyx_n_s__strip; static PyObject *__pyx_n_s__sys; static PyObject *__pyx_n_s__t; static PyObject *__pyx_n_s__tabixfile; static PyObject *__pyx_n_s__type; static PyObject *__pyx_n_s__upper; static PyObject *__pyx_n_s__v; static PyObject *__pyx_n_s__validate; static PyObject *__pyx_n_s__value; static PyObject *__pyx_n_s__values; static PyObject *__pyx_n_s__var; static PyObject *__pyx_n_s__vcf; static PyObject *__pyx_n_s__vcffile; static PyObject *__pyx_n_s__version; static PyObject *__pyx_n_s__warnerror; static PyObject *__pyx_n_s__write; static PyObject *__pyx_n_s__write_data; static PyObject *__pyx_n_s__write_header; static PyObject *__pyx_n_s__write_heading; static PyObject *__pyx_n_s__writeheader; static PyObject *__pyx_n_s__x; static PyObject *__pyx_n_s__y; static PyObject *__pyx_n_s__zip; static PyObject *__pyx_int_0; static PyObject *__pyx_int_1; static PyObject *__pyx_int_2; static PyObject *__pyx_int_3; static PyObject *__pyx_int_4; static PyObject *__pyx_int_5; static PyObject *__pyx_int_6; static PyObject *__pyx_int_7; static PyObject *__pyx_int_8; static PyObject *__pyx_int_9; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_int_10; static PyObject *__pyx_int_11; static PyObject *__pyx_int_12; static PyObject *__pyx_int_13; static PyObject *__pyx_int_14; static PyObject *__pyx_int_15; static PyObject *__pyx_int_16; static PyObject *__pyx_int_17; static PyObject *__pyx_int_18; static PyObject *__pyx_int_19; static PyObject *__pyx_int_20; static PyObject *__pyx_int_21; static PyObject *__pyx_int_22; static PyObject *__pyx_int_23; static PyObject *__pyx_int_24; static PyObject *__pyx_int_25; static PyObject *__pyx_int_26; static PyObject *__pyx_int_27; static PyObject *__pyx_int_28; static PyObject *__pyx_int_29; static PyObject *__pyx_int_30; static PyObject *__pyx_int_31; static PyObject *__pyx_int_32; static PyObject *__pyx_int_33; static PyObject *__pyx_int_40; static PyObject *__pyx_int_100; static PyObject *__pyx_int_3000000000; static PyObject *__pyx_k_tuple_3; static PyObject *__pyx_k_tuple_5; static PyObject *__pyx_k_tuple_7; static PyObject *__pyx_k_tuple_10; static PyObject *__pyx_k_tuple_12; static PyObject *__pyx_k_tuple_13; static PyObject *__pyx_k_tuple_15; static PyObject *__pyx_k_tuple_16; static PyObject *__pyx_k_tuple_17; static PyObject *__pyx_k_tuple_22; static PyObject *__pyx_k_tuple_23; static PyObject *__pyx_k_tuple_26; static PyObject *__pyx_k_tuple_29; static PyObject *__pyx_k_tuple_30; static PyObject *__pyx_k_tuple_31; static PyObject *__pyx_k_tuple_33; static PyObject *__pyx_k_tuple_34; static PyObject *__pyx_k_tuple_35; static PyObject *__pyx_k_tuple_42; static PyObject *__pyx_k_tuple_43; static PyObject *__pyx_k_tuple_44; static PyObject *__pyx_k_tuple_45; static PyObject *__pyx_k_tuple_46; static PyObject *__pyx_k_tuple_47; static PyObject *__pyx_k_tuple_48; static PyObject *__pyx_k_tuple_49; static PyObject *__pyx_k_tuple_51; static PyObject *__pyx_k_tuple_52; static PyObject *__pyx_k_tuple_62; static PyObject *__pyx_k_tuple_63; static PyObject *__pyx_k_tuple_77; static PyObject *__pyx_k_tuple_78; static PyObject *__pyx_k_tuple_86; static PyObject *__pyx_k_tuple_87; static PyObject *__pyx_k_tuple_89; static PyObject *__pyx_k_tuple_97; static PyObject *__pyx_k_tuple_98; static PyObject *__pyx_k_tuple_99; static PyObject *__pyx_k_tuple_103; static PyObject *__pyx_k_tuple_107; static PyObject *__pyx_k_tuple_108; static PyObject *__pyx_k_tuple_109; static PyObject *__pyx_k_tuple_110; static PyObject *__pyx_k_tuple_111; static PyObject *__pyx_k_tuple_112; static PyObject *__pyx_k_tuple_113; static PyObject *__pyx_k_tuple_117; static PyObject *__pyx_k_tuple_119; static PyObject *__pyx_k_tuple_120; static PyObject *__pyx_k_tuple_122; static PyObject *__pyx_k_tuple_124; static PyObject *__pyx_k_tuple_127; static PyObject *__pyx_k_tuple_129; static PyObject *__pyx_k_tuple_131; static PyObject *__pyx_k_tuple_132; static PyObject *__pyx_k_tuple_136; static PyObject *__pyx_k_tuple_139; static PyObject *__pyx_k_tuple_174; static PyObject *__pyx_k_tuple_176; static PyObject *__pyx_k_tuple_178; static PyObject *__pyx_k_tuple_179; static PyObject *__pyx_k_tuple_181; static PyObject *__pyx_k_tuple_183; static PyObject *__pyx_k_tuple_185; static PyObject *__pyx_k_tuple_187; static PyObject *__pyx_k_tuple_189; static PyObject *__pyx_k_tuple_191; static PyObject *__pyx_k_tuple_193; static PyObject *__pyx_k_tuple_195; static PyObject *__pyx_k_tuple_197; static PyObject *__pyx_k_tuple_199; static PyObject *__pyx_k_tuple_201; static PyObject *__pyx_k_tuple_203; static PyObject *__pyx_k_tuple_205; static PyObject *__pyx_k_tuple_207; static PyObject *__pyx_k_tuple_209; static PyObject *__pyx_k_tuple_211; static PyObject *__pyx_k_tuple_213; static PyObject *__pyx_k_tuple_215; static PyObject *__pyx_k_tuple_217; static PyObject *__pyx_k_tuple_219; static PyObject *__pyx_k_tuple_221; static PyObject *__pyx_k_tuple_223; static PyObject *__pyx_k_tuple_225; static PyObject *__pyx_k_tuple_227; static PyObject *__pyx_k_tuple_229; static PyObject *__pyx_k_tuple_231; static PyObject *__pyx_k_tuple_233; static PyObject *__pyx_k_tuple_235; static PyObject *__pyx_k_tuple_237; static PyObject *__pyx_k_tuple_239; static PyObject *__pyx_k_tuple_241; static PyObject *__pyx_k_tuple_243; static PyObject *__pyx_k_tuple_245; static PyObject *__pyx_k_tuple_247; static PyObject *__pyx_k_tuple_249; static PyObject *__pyx_k_tuple_251; static PyObject *__pyx_k_tuple_253; static PyObject *__pyx_k_tuple_255; static PyObject *__pyx_k_tuple_257; static PyObject *__pyx_k_tuple_258; static PyObject *__pyx_k_codeobj_133; static PyObject *__pyx_k_codeobj_137; static PyObject *__pyx_k_codeobj_175; static PyObject *__pyx_k_codeobj_177; static PyObject *__pyx_k_codeobj_180; static PyObject *__pyx_k_codeobj_182; static PyObject *__pyx_k_codeobj_184; static PyObject *__pyx_k_codeobj_186; static PyObject *__pyx_k_codeobj_188; static PyObject *__pyx_k_codeobj_190; static PyObject *__pyx_k_codeobj_192; static PyObject *__pyx_k_codeobj_194; static PyObject *__pyx_k_codeobj_196; static PyObject *__pyx_k_codeobj_198; static PyObject *__pyx_k_codeobj_200; static PyObject *__pyx_k_codeobj_202; static PyObject *__pyx_k_codeobj_204; static PyObject *__pyx_k_codeobj_206; static PyObject *__pyx_k_codeobj_208; static PyObject *__pyx_k_codeobj_210; static PyObject *__pyx_k_codeobj_212; static PyObject *__pyx_k_codeobj_214; static PyObject *__pyx_k_codeobj_216; static PyObject *__pyx_k_codeobj_218; static PyObject *__pyx_k_codeobj_220; static PyObject *__pyx_k_codeobj_222; static PyObject *__pyx_k_codeobj_224; static PyObject *__pyx_k_codeobj_226; static PyObject *__pyx_k_codeobj_228; static PyObject *__pyx_k_codeobj_230; static PyObject *__pyx_k_codeobj_232; static PyObject *__pyx_k_codeobj_234; static PyObject *__pyx_k_codeobj_236; static PyObject *__pyx_k_codeobj_238; static PyObject *__pyx_k_codeobj_240; static PyObject *__pyx_k_codeobj_242; static PyObject *__pyx_k_codeobj_244; static PyObject *__pyx_k_codeobj_246; static PyObject *__pyx_k_codeobj_248; static PyObject *__pyx_k_codeobj_250; static PyObject *__pyx_k_codeobj_252; static PyObject *__pyx_k_codeobj_254; static PyObject *__pyx_k_codeobj_256; static PyObject *__pyx_k_codeobj_259; /* Python wrapper */ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyMethodDef __pyx_mdef_5pysam_4cvcf_1get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pw_5pysam_4cvcf_1get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_chrom = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_fa = 0; static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_sequence (wrapper)", 0); __pyx_self = __pyx_self; { PyObject* values[4] = {0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom); if (likely(values[0])) kw_args--; else goto __pyx_L5_argtuple_error; case 1: values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); if (likely(values[1])) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); if (likely(values[2])) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); 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return o; } static void __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; Py_XDECREF(p->vcf); __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o); } static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) { e = __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a); if (e) return e; } if (p->vcf) { e = (*v)(p->vcf, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf_VCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; PyObject* tmp; if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) { __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o); } tmp = ((PyObject*)p->vcf); p->vcf = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5pysam_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) { PyObject *r; PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); Py_DECREF(x); return r; } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_4cvcf_VCFRecord[] = { {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_5pysam_4cvcf_9VCFRecord_5error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_9VCFRecord_4error)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_4cvcf_VCFRecord[] = { {(char *)"contig", __pyx_getprop_5pysam_4cvcf_9VCFRecord_contig, 0, 0, 0}, {(char *)"pos", __pyx_getprop_5pysam_4cvcf_9VCFRecord_pos, 0, 0, 0}, {(char *)"id", __pyx_getprop_5pysam_4cvcf_9VCFRecord_id, 0, 0, 0}, {(char *)"ref", __pyx_getprop_5pysam_4cvcf_9VCFRecord_ref, 0, 0, 0}, {(char *)"alt", __pyx_getprop_5pysam_4cvcf_9VCFRecord_alt, 0, 0, 0}, {(char *)"qual", __pyx_getprop_5pysam_4cvcf_9VCFRecord_qual, 0, 0, 0}, {(char *)"filter", __pyx_getprop_5pysam_4cvcf_9VCFRecord_filter, 0, 0, 0}, {(char *)"info", __pyx_getprop_5pysam_4cvcf_9VCFRecord_info, 0, 0, 0}, {(char *)"format", __pyx_getprop_5pysam_4cvcf_9VCFRecord_format, 0, 0, 0}, {(char *)"samples", __pyx_getprop_5pysam_4cvcf_9VCFRecord_samples, 0, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_VCFRecord = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = { __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5pysam_4cvcf_VCFRecord, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = { __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*mp_length*/ __pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_4cvcf_VCFRecord = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.cvcf.VCFRecord"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_4cvcf_VCFRecord), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord, /*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_VCFRecord, /*tp_as_number*/ &__pyx_tp_as_sequence_VCFRecord, /*tp_as_sequence*/ &__pyx_tp_as_mapping_VCFRecord, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_VCFRecord, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("vcf record.\n\n initialized from data and vcf meta \n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_4cvcf_VCFRecord, /*tp_traverse*/ __pyx_tp_clear_5pysam_4cvcf_VCFRecord, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_4cvcf_VCFRecord, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_4cvcf_VCFRecord, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_4cvcf_VCFRecord, /*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_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p; PyObject *o = __pyx_ptype_5pysam_6ctabix_Parser->tp_new(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o); p->vcffile = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; Py_XDECREF(p->vcffile); __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o); } static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; if (__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) { e = __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e; } if (p->vcffile) { e = (*v)(p->vcffile, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; PyObject* tmp; if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) { __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } tmp = ((PyObject*)p->vcffile); p->vcffile = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_4cvcf_asVCFRecord[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asVCFRecord = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_asVCFRecord = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_asVCFRecord = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_4cvcf_asVCFRecord = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.cvcf.asVCFRecord"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_4cvcf_asVCFRecord), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord, /*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_asVCFRecord, /*tp_as_number*/ &__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asVCFRecord, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/ __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord, /*tp_traverse*/ __pyx_tp_clear_5pysam_4cvcf_asVCFRecord, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_4cvcf_asVCFRecord, /*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*/ __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_4cvcf_asVCFRecord, /*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_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o); p->__pyx_v_alt = 0; return o; } static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; Py_XDECREF(p->__pyx_v_alt); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; if (p->__pyx_v_alt) { e = (*v)(p->__pyx_v_alt, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_v_alt); p->__pyx_v_alt = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__parse_data = { 0, /*nb_add*/ 0, /*nb_subtract*/ 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tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (XDECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_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, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); Py_XINCREF(value); Py_XINCREF(tb); if (tb == Py_None) { Py_DECREF(tb); tb = 0; } else if (tb != NULL && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } if (value == NULL) { value = Py_None; Py_INCREF(value); } #if PY_VERSION_HEX < 0x02050000 if (!PyClass_Check(type)) #else if (!PyType_Check(type)) #endif { if (value != Py_None) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } Py_DECREF(value); value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (!PyExceptionClass_Check(type)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } if (!value) { value = PyObject_CallObject(type, NULL); } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: return; } #endif static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) { return PyFloat_AsDouble(obj); } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) { #if PY_MAJOR_VERSION >= 3 float_value = PyFloat_FromString(obj); #else float_value = PyFloat_FromString(obj, 0); #endif } else { PyObject* args = PyTuple_New(1); if (unlikely(!args)) goto bad; PyTuple_SET_ITEM(args, 0, obj); float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0); PyTuple_SET_ITEM(args, 0, 0); Py_DECREF(args); } if (likely(float_value)) { double value = PyFloat_AS_DOUBLE(float_value); Py_DECREF(float_value); return value; } bad: return (double)-1; } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected); } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; } static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t q = a / b; Py_ssize_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { /* try package relative import first */ PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: Py_XDECREF(empty_list); Py_XDECREF(py_import); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) { #if PY_MAJOR_VERSION < 3 PyErr_Format(PyExc_ImportError, "cannot import name %.230s", PyString_AsString(name)); #else PyErr_Format(PyExc_ImportError, "cannot import name %S", name); #endif } static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; /* Default metaclass */ #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = PyObject_GetAttrString(base, (char *)"__class__"); if (!metaclass) { PyErr_Clear(); metaclass = (PyObject*) Py_TYPE(base); } } else { metaclass = (PyObject *) &PyClass_Type; } #else if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = (PyObject*) Py_TYPE(base); } else { metaclass = (PyObject *) &PyType_Type; } #endif Py_INCREF(metaclass); return metaclass; } static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *modname) { PyObject *result; PyObject *metaclass; if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; /* Python2 __metaclass__ */ metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { Py_INCREF(metaclass); } else { metaclass = __Pyx_FindPy2Metaclass(bases); } result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL); Py_DECREF(metaclass); return result; } static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (op->func_doc == NULL && op->func.m_ml->ml_doc) { #if PY_MAJOR_VERSION >= 3 op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); #else op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); #endif } if (op->func_doc == 0) { Py_INCREF(Py_None); return Py_None; } Py_INCREF(op->func_doc); return op->func_doc; } static int __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp = op->func_doc; if (value == NULL) op->func_doc = Py_None; /* Mark as deleted */ else op->func_doc = value; Py_INCREF(op->func_doc); Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) { if (op->func_name == NULL) { #if PY_MAJOR_VERSION >= 3 op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); #else op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); #endif } Py_INCREF(op->func_name); return op->func_name; } static int __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (value == NULL || !PyUnicode_Check(value)) { #else if (value == NULL || !PyString_Check(value)) { #endif PyErr_SetString(PyExc_TypeError, "__name__ must be set to a string object"); return -1; } tmp = op->func_name; Py_INCREF(value); op->func_name = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) { PyObject *self; self = m->func_closure; if (self == NULL) self = Py_None; Py_INCREF(self); return self; } static PyObject * __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) { if (op->func_dict == NULL) { op->func_dict = PyDict_New(); if (op->func_dict == NULL) return NULL; } Py_INCREF(op->func_dict); return op->func_dict; } static int __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; if (value == NULL) { PyErr_SetString(PyExc_TypeError, "function's dictionary may not be deleted"); return -1; } if (!PyDict_Check(value)) { PyErr_SetString(PyExc_TypeError, "setting function's dictionary to a non-dict"); return -1; } tmp = op->func_dict; Py_INCREF(value); op->func_dict = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) { PyObject* dict = PyModule_GetDict(__pyx_m); Py_XINCREF(dict); return dict; } static PyObject * __Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) { Py_INCREF(Py_None); return Py_None; } static PyObject * __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) { PyObject* result = (op->func_code) ? op->func_code : Py_None; Py_INCREF(result); return result; } static PyObject * __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { if (op->defaults_tuple) { Py_INCREF(op->defaults_tuple); return op->defaults_tuple; } if (op->defaults_getter) { PyObject *res = op->defaults_getter((PyObject *) op); if (res) { Py_INCREF(res); op->defaults_tuple = res; } return res; } Py_INCREF(Py_None); return Py_None; } static PyGetSetDef __pyx_CyFunction_getsets[] = { {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {0, 0, 0, 0, 0} }; #ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ #define PY_WRITE_RESTRICTED WRITE_RESTRICTED #endif static PyMemberDef __pyx_CyFunction_members[] = { {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, {0, 0, 0, 0, 0} }; static PyObject * __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromString(m->func.m_ml->ml_name); #else return PyString_FromString(m->func.m_ml->ml_name); #endif } static PyMethodDef __pyx_CyFunction_methods[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, {0, 0, 0, 0} }; static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject *closure, PyObject *module, PyObject* code) { __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); if (op == NULL) return NULL; op->flags = flags; op->func_weakreflist = NULL; op->func.m_ml = ml; op->func.m_self = (PyObject *) op; Py_XINCREF(closure); op->func_closure = closure; Py_XINCREF(module); op->func.m_module = module; op->func_dict = NULL; op->func_name = NULL; op->func_doc = NULL; op->func_classobj = NULL; Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_getter = NULL; PyObject_GC_Track(op); return (PyObject *) op; } static int __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) { Py_CLEAR(m->func_closure); Py_CLEAR(m->func.m_module); Py_CLEAR(m->func_dict); Py_CLEAR(m->func_name); Py_CLEAR(m->func_doc); Py_CLEAR(m->func_code); Py_CLEAR(m->func_classobj); Py_CLEAR(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_XDECREF(pydefaults[i]); PyMem_Free(m->defaults); m->defaults = NULL; } return 0; } static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) { PyObject_GC_UnTrack(m); if (m->func_weakreflist != NULL) PyObject_ClearWeakRefs((PyObject *) m); __Pyx_CyFunction_clear(m); PyObject_GC_Del(m); } static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) { Py_VISIT(m->func_closure); Py_VISIT(m->func.m_module); Py_VISIT(m->func_dict); Py_VISIT(m->func_name); Py_VISIT(m->func_doc); Py_VISIT(m->func_code); Py_VISIT(m->func_classobj); Py_VISIT(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_VISIT(pydefaults[i]); } return 0; } static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { Py_INCREF(func); return func; } if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { if (type == NULL) type = (PyObject *)(Py_TYPE(obj)); return PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); } if (obj == Py_None) obj = NULL; return PyMethod_New(func, obj, type); } static PyObject* __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) { PyObject *func_name = __Pyx_CyFunction_get_name(op); #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromFormat("", func_name, (void *)op); #else return PyString_FromFormat("", PyString_AsString(func_name), (void *)op); #endif } static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ __Pyx_PyCFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_CyFunction_methods, /*tp_methods*/ __pyx_CyFunction_members, /*tp_members*/ __pyx_CyFunction_getsets, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ __Pyx_CyFunction_descr_get, /*tp_descr_get*/ 0, /*tp_descr_set*/ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static int __Pyx_CyFunction_init(void) { if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) return PyErr_NoMemory(); memset(m->defaults, 0, sizeof(size)); m->defaults_pyobjects = pyobjects; return m->defaults; } static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults_tuple = tuple; Py_INCREF(tuple); } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint32_t) == sizeof(char)) || (sizeof(uint32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint32_t) == sizeof(int)) || (sizeof(uint32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { if (s1 == s2) { return (equals == Py_EQ); } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyBytes_GET_SIZE(s1) == 1) { if (equals == Py_EQ) return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]); else return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]); } else { int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1)); return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } } static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { if (s1 == s2) { return (equals == Py_EQ); } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { #if CYTHON_PEP393_ENABLED if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) return -1; if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { return (equals == Py_NE); } else if (PyUnicode_GET_LENGTH(s1) == 1) { Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); #else if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyUnicode_GET_SIZE(s1) == 1) { Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); #endif } else { int result = PyUnicode_Compare(s1, s2); if ((result == -1) && unlikely(PyErr_Occurred())) return -1; return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = *type; tstate->exc_value = *value; tstate->exc_traceback = *tb; *type = tmp_type; *value = tmp_value; *tb = tmp_tb; } static PyObject *__Pyx_Generator_Next(PyObject *self); static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); static PyObject *__Pyx_Generator_Close(PyObject *self); static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) { PyObject *exc_type = self->exc_type; PyObject *exc_value = self->exc_value; PyObject *exc_traceback = self->exc_traceback; self->exc_type = NULL; self->exc_value = NULL; self->exc_traceback = NULL; Py_XDECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_traceback); } static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) { PyObject *retval; if (unlikely(self->is_running)) { PyErr_SetString(PyExc_ValueError, "generator already executing"); return NULL; } if (unlikely(self->resume_label == 0)) { if (unlikely(value && value != Py_None)) { PyErr_SetString(PyExc_TypeError, "can't send non-None value to a " "just-started generator"); return NULL; } } if (unlikely(self->resume_label == -1)) { PyErr_SetNone(PyExc_StopIteration); return NULL; } if (value) __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); else __Pyx_Generator_ExceptionClear(self); self->is_running = 1; retval = self->body((PyObject *) self, value); self->is_running = 0; if (retval) __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); else __Pyx_Generator_ExceptionClear(self); return retval; } static PyObject *__Pyx_Generator_Next(PyObject *self) { return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None); } static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value); } static PyObject *__Pyx_Generator_Close(PyObject *self) { __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; PyObject *retval; #if PY_VERSION_HEX < 0x02050000 PyErr_SetNone(PyExc_StopIteration); #else PyErr_SetNone(PyExc_GeneratorExit); #endif retval = __Pyx_Generator_SendEx(generator, NULL); if (retval) { Py_DECREF(retval); PyErr_SetString(PyExc_RuntimeError, "generator ignored GeneratorExit"); return NULL; } #if PY_VERSION_HEX < 0x02050000 if (PyErr_ExceptionMatches(PyExc_StopIteration)) #else if (PyErr_ExceptionMatches(PyExc_StopIteration) || PyErr_ExceptionMatches(PyExc_GeneratorExit)) #endif { PyErr_Clear(); /* ignore these errors */ Py_INCREF(Py_None); return Py_None; } return NULL; } static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) { __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; __Pyx_Raise(typ, val, tb, NULL); return __Pyx_Generator_SendEx(generator, NULL); } static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_VISIT(gen->closure); Py_VISIT(gen->classobj); Py_VISIT(gen->exc_type); Py_VISIT(gen->exc_value); Py_VISIT(gen->exc_traceback); return 0; } static void __Pyx_Generator_dealloc(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject_GC_UnTrack(gen); if (gen->gi_weakreflist != NULL) PyObject_ClearWeakRefs(self); PyObject_GC_Track(self); if (gen->resume_label > 0) { Py_TYPE(gen)->tp_del(self); if (self->ob_refcnt > 0) return; /* resurrected. :( */ } PyObject_GC_UnTrack(self); Py_CLEAR(gen->closure); Py_CLEAR(gen->classobj); Py_CLEAR(gen->exc_type); Py_CLEAR(gen->exc_value); Py_CLEAR(gen->exc_traceback); PyObject_GC_Del(gen); } static void __Pyx_Generator_del(PyObject *self) { PyObject *res; PyObject *error_type, *error_value, *error_traceback; __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; if (gen->resume_label <= 0) return ; assert(self->ob_refcnt == 0); self->ob_refcnt = 1; __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); res = __Pyx_Generator_Close(self); if (res == NULL) PyErr_WriteUnraisable(self); else Py_DECREF(res); __Pyx_ErrRestore(error_type, error_value, error_traceback); /* Undo the temporary resurrection; can't use DECREF here, it would * cause a recursive call. */ assert(self->ob_refcnt > 0); if (--self->ob_refcnt == 0) return; /* this is the normal path out */ /* close() resurrected it! Make it look like the original Py_DECREF * never happened. */ { Py_ssize_t refcnt = self->ob_refcnt; _Py_NewReference(self); self->ob_refcnt = refcnt; } assert(PyType_IS_GC(self->ob_type) && _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so * we need to undo that. */ _Py_DEC_REFTOTAL; /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object * chain, so no more to do there. * If COUNT_ALLOCS, the original decref bumped tp_frees, and * _Py_NewReference bumped tp_allocs: both of those need to be * undone. */ #ifdef COUNT_ALLOCS --self->ob_type->tp_frees; --self->ob_type->tp_allocs; #endif } static PyMemberDef __pyx_Generator_memberlist[] = { {(char *) "gi_running", T_INT, offsetof(__pyx_GeneratorObject, is_running), READONLY, NULL}, {0, 0, 0, 0, 0} }; static PyMethodDef __pyx_Generator_methods[] = { {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0}, {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0}, {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, {0, 0, 0, 0} }; static PyTypeObject __pyx_GeneratorType = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("generator"), /*tp_name*/ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ PyObject_GenericGetAttr, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */ PyObject_SelfIter, /*tp_iter*/ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/ __pyx_Generator_methods, /*tp_methods*/ __pyx_Generator_memberlist, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ __Pyx_Generator_del, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure) { __pyx_GeneratorObject *gen = PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType); if (gen == NULL) return NULL; gen->body = body; gen->closure = closure; Py_XINCREF(closure); gen->is_running = 0; gen->resume_label = 0; gen->classobj = NULL; gen->exc_type = NULL; gen->exc_value = NULL; gen->exc_traceback = NULL; gen->gi_weakreflist = NULL; PyObject_GC_Track(gen); return gen; } static int __pyx_Generator_init(void) { return PyType_Ready(&__pyx_GeneratorType); } static 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; } #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, 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; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } 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 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #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; 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 static void* __Pyx_GetVtable(PyObject *dict) { void* ptr; PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__"); if (!ob) goto bad; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) ptr = PyCapsule_GetPointer(ob, 0); #else ptr = PyCObject_AsVoidPtr(ob); #endif if (!ptr && !PyErr_Occurred()) PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type"); Py_DECREF(ob); return ptr; bad: Py_XDECREF(ob); return NULL; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static 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; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 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,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); 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,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } /* Type Conversion Functions */ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */