/* Generated by Cython 0.16 on Tue Jan 15 06:50:01 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; 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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_6ctabix_Parser; struct __pyx_obj_5pysam_6ctabix_asTuple; struct __pyx_obj_5pysam_6ctabix_asVCF; 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_10TabProxies_GTFProxy; struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator; /* "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; }; /* "pysam/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; }; /* "pysam/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; }; /* "pysam/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; }; /* "pysam/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/ctabix.pxd":190 * cdef tabix_t * tabixfile * * cdef class Parser: # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_Parser { PyObject_HEAD }; /* "pysam/ctabix.pxd":193 * pass * * cdef class asTuple(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asTuple { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "pysam/ctabix.pxd":202 * pass * * cdef class asVCF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asVCF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "pysam/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; }; /* "pysam/ctabix.pxd":199 * pass * * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asBed { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "pysam/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; }; /* "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; }; /* "pysam/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; }; /* "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/ctabix.pyx":709 * ## Iterators for parsing through unindexed files. * ######################################################### * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< * '''iterate over ``infile``. * */ 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; /* "pysam/ctabix.pyx":771 * return self.__cnext__() * * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< * '''iterate over ``infile``. * */ 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 (!j) return NULL; r = PyObject_GetItem(o, j); Py_DECREF(j); return r; } #define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_List_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { if (likely(o != Py_None)) { if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { PyObject *r = PyList_GET_ITEM(o, i); Py_INCREF(r); return r; } else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); Py_INCREF(r); return r; } } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } #define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Tuple_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { if (likely(o != Py_None)) { if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { PyObject *r = PyTuple_GET_ITEM(o, i); 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} } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } 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 int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); /*proto*/ 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 int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ 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 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; #define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code) static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, int flags, PyObject *self, PyObject *module, PyObject* code); static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, size_t size, int pyobjects); static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, PyObject *tuple); static int __Pyx_CyFunction_init(void); static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); 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static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static int __Pyx_check_binary_version(void); static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static void* __Pyx_GetVtable(PyObject *dict); /*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.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 'cpython.version' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'cpython.exc' */ /* Module declarations from 'cpython.module' */ /* Module declarations from 'cpython.mem' */ /* Module declarations from 'cpython.tuple' */ /* Module declarations from 'cpython.list' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from 'cpython.sequence' */ /* Module declarations from 'cpython.mapping' */ /* Module declarations from 'cpython.iterator' */ /* Module declarations from 'cpython.type' */ /* Module declarations from 'cpython.number' */ /* Module declarations from 'cpython.int' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.bool' */ static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0; /* Module declarations from 'cpython.long' */ /* Module declarations from 'cpython.float' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.complex' */ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from 'cpython.string' */ /* Module declarations from 'cpython.unicode' */ /* Module declarations from 'cpython.dict' */ /* Module declarations from 'cpython.instance' */ /* Module declarations from 'cpython.function' */ /* Module declarations from 'cpython.method' */ /* Module declarations from 'cpython.weakref' */ /* Module declarations from 'cpython.getargs' */ /* Module declarations from 'cpython.pythread' */ /* Module declarations from 'cpython.pystate' */ /* Module declarations from 'cpython.cobject' */ /* Module declarations from 'cpython.oldbuffer' */ /* Module declarations from 'cpython.set' */ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.bytes' */ /* Module declarations from 'cpython.pycapsule' */ /* Module declarations from 'cpython' */ /* 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; static PyObject *__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = 0; static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *); /*proto*/ #define __Pyx_MODULE_NAME "pysam.ctabix" int __pyx_module_is_main_pysam__ctabix = 0; /* Implementation of 'pysam.ctabix' */ static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_OSError; static PyObject *__pyx_builtin_ord; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_MemoryError; static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_10close(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */ static int __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "invalid file opening mode `%s`"; static char __pyx_k_6[] = ".tbi"; static char __pyx_k_7[] = "http:"; static char __pyx_k_9[] = "ftp:"; static char __pyx_k_12[] = "writing to tabix files not implemented"; static char __pyx_k_14[] = "file `%s` not found"; static char __pyx_k_15[] = "index `%s` not found"; static char __pyx_k_16[] = "could not open file `%s`"; static char __pyx_k_17[] = "%s:%i-%i"; static char __pyx_k_18[] = "invalid region `%s`"; static char __pyx_k_19[] = "invalid region: start (%i) > end (%i)"; static char __pyx_k_20[] = "start out of range (%i)"; static char __pyx_k_21[] = "end out of range (%i)"; static char __pyx_k_22[] = "I/O operation on closed file"; static char __pyx_k_25[] = "malformatted query or wrong sequence name.\n"; static char __pyx_k_27[] = "can't open header.\n"; static char __pyx_k_31[] = "Filename '%s' already exists, use *force* to overwrite"; static char __pyx_k_32[] = "could not open '%s' for writing"; static char __pyx_k_34[] = "could not open '%s' for reading"; static char __pyx_k_36[] = "writing failed"; static char __pyx_k_40[] = "#"; static char __pyx_k_42[] = "No such file '%s'"; static char __pyx_k_43[] = "neither preset nor seq_col,start_col and end_col given"; static char __pyx_k_45[] = ".gz"; static char __pyx_k_47[] = "Filename '%s.tbi' already exists, use *force* to overwrite"; static char __pyx_k_49[] = "unknown preset '%s', valid presets are '%s'"; static char __pyx_k_50[] = ","; static char __pyx_k_51[] = "I/O operation on closed file."; static char __pyx_k_54[] = "incomplete line at %s"; static char __pyx_k_58[] = "tabix_generic_iterator"; static char __pyx_k_59[] = "filename associated with this object."; static char __pyx_k_60[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n "; static char __pyx_k_61[] = "chromosome names"; static char __pyx_k_62[] = "getfilesystemencoding"; static char __pyx_k_65[] = "/home/andreas/devel/pysam/pysam/ctabix.pyx"; static char __pyx_k_66[] = "pysam.ctabix"; static char __pyx_k_77[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; static char __pyx_k_80[] = "tabix_inplace_iterator"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__r[] = "r"; static char __pyx_k__s[] = "s"; static char __pyx_k__w[] = "w"; static char __pyx_k__fn[] = "fn"; static char __pyx_k__fp[] = "fp"; static char __pyx_k__io[] = "io"; static char __pyx_k__os[] = "os"; static char __pyx_k__bed[] = "bed"; static char __pyx_k__cpy[] = "cpy"; static char __pyx_k__end[] = "end"; static char __pyx_k__gff[] = "gff"; static char __pyx_k__len[] = "len"; static char __pyx_k__ord[] = "ord"; static char __pyx_k__sam[] = "sam"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__tid[] = "tid"; static char __pyx_k__vcf[] = "vcf"; static char __pyx_k__conf[] = "conf"; static char __pyx_k__gzip[] = "gzip"; static char __pyx_k__join[] = "join"; static char __pyx_k__line[] = "line"; static char __pyx_k__mode[] = "mode"; static char __pyx_k__next[] = "next"; static char __pyx_k__path[] = "path"; static char __pyx_k__self[] = "self"; static char __pyx_k___open[] = "_open"; static char __pyx_k__asBed[] = "asBed"; static char __pyx_k__asGTF[] = "asGTF"; static char __pyx_k__asVCF[] = "asVCF"; static char __pyx_k__ascii[] = "ascii"; static char __pyx_k__close[] = "close"; static char __pyx_k__force[] = "force"; static char __pyx_k__start[] = "start"; static char __pyx_k__types[] = "types"; static char __pyx_k__Parser[] = "Parser"; static char __pyx_k__buffer[] = "buffer"; static char __pyx_k__closed[] = "closed"; static char __pyx_k__ctypes[] = "ctypes"; static char __pyx_k__decode[] = "decode"; static char __pyx_k__encode[] = "encode"; static char __pyx_k__exists[] = "exists"; static char __pyx_k__fd_src[] = "fd_src"; static char __pyx_k__infile[] = "infile"; static char __pyx_k__nbytes[] = "nbytes"; static char __pyx_k__parser[] = "parser"; static char __pyx_k__pileup[] = "pileup"; static char __pyx_k__preset[] = "preset"; static char __pyx_k__psltbl[] = "psltbl"; static char __pyx_k__region[] = "region"; static char __pyx_k__struct[] = "struct"; static char __pyx_k__unlink[] = "unlink"; static char __pyx_k__IOError[] = "IOError"; static char __pyx_k__OSError[] = "OSError"; static char __pyx_k__PYTHON3[] = "PYTHON3"; static char __pyx_k____all__[] = "__all__"; static char __pyx_k___isOpen[] = "_isOpen"; static char __pyx_k__asTuple[] = "asTuple"; static char __pyx_k__end_col[] = "end_col"; static char __pyx_k__present[] = "present"; static char __pyx_k__seq_col[] = "seq_col"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k__O_RDONLY[] = "O_RDONLY"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____iter__[] = "__iter__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____next__[] = "__next__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__endswith[] = "endswith"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__readline[] = "readline"; static char __pyx_k__tempfile[] = "tempfile"; static char __pyx_k__Tabixfile[] = "Tabixfile"; static char __pyx_k__TypeError[] = "TypeError"; static char __pyx_k__conf_data[] = "conf_data"; static char __pyx_k__itertools[] = "itertools"; static char __pyx_k__meta_char[] = "meta_char"; static char __pyx_k__reference[] = "reference"; static char __pyx_k__start_col[] = "start_col"; static char __pyx_k__tabixfile[] = "tabixfile"; static char __pyx_k__zerobased[] = "zerobased"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__MemoryError[] = "MemoryError"; static char __pyx_k__WINDOW_SIZE[] = "WINDOW_SIZE"; static char __pyx_k__buffer_size[] = "buffer_size"; static char __pyx_k__filename_in[] = "filename_in"; static char __pyx_k__preset2conf[] = "preset2conf"; static char __pyx_k__tabix_index[] = "tabix_index"; static char __pyx_k___parseRegion[] = "_parseRegion"; static char __pyx_k__filename_out[] = "filename_out"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k__tabix_compress[] = "tabix_compress"; static char __pyx_k__tabix_iterator[] = "tabix_iterator"; 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static PySequenceMethods __pyx_tp_as_sequence_TabixIterator = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_TabixIterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_TabixIterator = { #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_6ctabix_TabixIterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_TabixIterator, /*tp_as_number*/ &__pyx_tp_as_sequence_TabixIterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_TabixIterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_TabixIterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("iterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_TabixIterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; if (__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixHeaderIterator[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = { 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_TabixHeaderIterator = { 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_TabixHeaderIterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = { #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_6ctabix_TabixHeaderIterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.TabixHeaderIterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator, /*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_TabixHeaderIterator, /*tp_as_number*/ &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_TabixHeaderIterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_TabixHeaderIterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator, /*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_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_Parser(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5pysam_6ctabix_Parser[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Parser = { 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_Parser = { 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_Parser = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Parser = { #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_6ctabix_Parser = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.Parser"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*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_Parser, /*tp_as_number*/ &__pyx_tp_as_sequence_Parser, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Parser, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Parser, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ 0, /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_Parser, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_Parser, /*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_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asTuple[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asTuple = { 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_asTuple = { 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_asTuple = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asTuple = { #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_6ctabix_asTuple = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asTuple"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*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_asTuple, /*tp_as_number*/ &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_6ctabix_7asTuple_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asTuple, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asTuple, /*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_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asGTF[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asGTF = { 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_asGTF = { 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_asGTF = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asGTF = { #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_6ctabix_asGTF = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asGTF"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*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_asGTF, /*tp_as_number*/ &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_6ctabix_5asGTF_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record with the following \n fields:\n\n contig\n contig\n feature\n feature\n source\n source\n start\n genomic start coordinate (0-based)\n end\n genomic end coordinate plus one (0-based)\n score\n feature score\n strand\n strand\n frame\n frame\n attributes\n attribute string.\n\n GTF formatted entries also defined the attributes:\n\n gene_id\n the gene identifier\n transcript_ind\n the transcript identifier\n \n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asGTF, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asGTF, /*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_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asBed[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asBed = { 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_asBed = { 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_asBed = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asBed = { #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_6ctabix_asBed = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asBed"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*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_asBed, /*tp_as_number*/ &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_6ctabix_5asBed_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n contig\n contig\n start\n genomic start coordinate (zero-based)\n end\n genomic end coordinate plus one (zero-based)\n name\n name of feature.\n score\n score of feature\n strand\n strand of feature\n thickStart\n thickStart\n thickEnd\n thickEnd\n itemRGB\n itemRGB\n blockCount\n number of bocks\n blockSizes\n ',' separated string of block sizes\n blockStarts\n ',' separated string of block genomic start positions\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceeding\n need to be defined as well.\n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asBed, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asBed, /*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_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asVCF[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asVCF = { 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_asVCF = { 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_asVCF = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asVCF = { #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_6ctabix_asVCF = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asVCF"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*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_asVCF, /*tp_as_number*/ &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_6ctabix_5asVCF_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n contig\n contig\n pos\n chromosomal position, zero-based\n id \n id\n ref\n reference\n alt\n alt\n qual\n qual\n filter\n filter\n info\n info\n format\n format specifier.\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample_genotype = vcf[1]\n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asVCF, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asVCF, /*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_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); if (__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o; { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_XDECREF(((PyObject *)p->parser)); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIteratorParsed[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_TabixIteratorParsed = { 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_TabixIteratorParsed = { 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_TabixIteratorParsed = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = { #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_6ctabix_TabixIteratorParsed = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.TabixIteratorParsed"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed, /*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_TabixIteratorParsed, /*tp_as_number*/ &__pyx_tp_as_sequence_TabixIteratorParsed, /*tp_as_sequence*/ &__pyx_tp_as_mapping_TabixIteratorParsed, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_TabixIteratorParsed, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterates over mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed, /*tp_traverse*/ __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_TabixIteratorParsed, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator __pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator; static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator; p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); if (__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o; { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_XDECREF(((PyObject *)p->parser)); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_tabix_inplace_iterator = { 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_tabix_inplace_iterator = { 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_tabix_inplace_iterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_tabix_inplace_iterator = { #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_6ctabix_tabix_inplace_iterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.tabix_inplace_iterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator, /*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_tabix_inplace_iterator, /*tp_as_number*/ &__pyx_tp_as_sequence_tabix_inplace_iterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_tabix_inplace_iterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_tabix_inplace_iterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not safe. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator, /*tp_traverse*/ __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator __pyx_vtable_5pysam_6ctabix_tabix_copy_iterator; static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator; p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); if (__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o; Py_XDECREF(((PyObject *)p->parser)); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_copy_iterator[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_tabix_copy_iterator = { 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_tabix_copy_iterator = { 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_tabix_copy_iterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_tabix_copy_iterator = { #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_6ctabix_tabix_copy_iterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.tabix_copy_iterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator, /*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_tabix_copy_iterator, /*tp_as_number*/ &__pyx_tp_as_sequence_tabix_copy_iterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_tabix_copy_iterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_tabix_copy_iterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not save. 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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 void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AS_STRING(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; } else { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { #else if (unlikely(!PyUnicode_Check(key))) { #endif goto invalid_keyword_type; } else { for (name = first_kw_arg; *name; name++) { #if PY_MAJOR_VERSION >= 3 if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && PyUnicode_Compare(**name, key) == 0) break; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) break; #endif } if (*name) { values[name-argnames] = value; } else { for (name=argnames; name != first_kw_arg; name++) { if (**name == key) goto arg_passed_twice; #if PY_MAJOR_VERSION >= 3 if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) goto arg_passed_twice; #endif } if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } } } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, **name); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static 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 int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; PyErr_NormalizeException(&local_type, &local_value, &local_tb); if (unlikely(tstate->curexc_type)) goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif *type = local_type; *value = local_value; *tb = local_tb; Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (XDECREF may run arbitrary code). */ 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_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 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 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 int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(int32_t) == sizeof(char)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (int32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(int32_t) == sizeof(short)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (int32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(int32_t) == sizeof(int)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (int32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(int32_t) == sizeof(long)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { int32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } return (int32_t)-1; } } 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 int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, 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_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 */