/* Generated by Cython 0.17.2 on Mon Sep 23 10:07:33 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 PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #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_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) #define PyInt_FromString PyLong_FromString #define PyInt_FromUnicode PyLong_FromUnicode #define PyInt_FromLong PyLong_FromLong #define PyInt_FromSize_t PyLong_FromSize_t #define PyInt_FromSsize_t PyLong_FromSsize_t #define PyInt_AsLong PyLong_AsLong #define PyInt_AS_LONG PyLong_AS_LONG #define PyInt_AsSsize_t PyLong_AsSsize_t #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) #else #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) #endif #ifndef __PYX_EXTERN_C #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" #else #define __PYX_EXTERN_C extern #endif #endif #if defined(WIN32) || defined(MS_WINDOWS) #define _USE_MATH_DEFINES #endif #include #define __PYX_HAVE__variant #define __PYX_HAVE_API__variant #include "string.h" #include "stdlib.h" #include "stdio.h" #include "ctype.h" #include "unistd.h" #include "razf.h" #include "stdint.h" #include "bam.h" #include "sam.h" #include "pysam_util.h" #include "math.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif /* inline attribute */ #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ #elif defined(_MSC_VER) #define CYTHON_INLINE __inline #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else #define CYTHON_INLINE #endif #endif /* unused attribute */ #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif #endif typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ /* Type Conversion Predeclarations */ #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) #define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) #define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; static const char *__pyx_f[] = { "variant.pyx", "variant.pxd", "fastafile.pxd", "samtoolsWrapper.pxd", "bamfileutils.pxd", }; /*--- Type declarations ---*/ struct __pyx_obj_7variant_VariantCandidateGenerator; struct __pyx_obj_9fastafile_FastaFile; struct __pyx_obj_15samtoolsWrapper_AlignedRead; struct __pyx_obj_15samtoolsWrapper_IteratorRow; struct __pyx_obj_15samtoolsWrapper_Samfile; struct __pyx_obj_15samtoolsWrapper_IteratorRowAll; struct __pyx_obj_9fastafile_FastaIndex; struct __pyx_obj_12bamfileutils_MultiBamFileReader; struct __pyx_obj_12bamfileutils_MultiBamFileIterator; struct __pyx_obj_7variant_Variant; struct __pyx_obj_12bamfileutils_BamFileIterator; struct __pyx_opt_args_15samtoolsWrapper_7Samfile__open; struct __pyx_opt_args_15samtoolsWrapper_7Samfile__parseRegion; struct __pyx_t_15samtoolsWrapper_cAlignedRead; typedef struct __pyx_t_15samtoolsWrapper_cAlignedRead __pyx_t_15samtoolsWrapper_cAlignedRead; /* "samtoolsWrapper.pxd":254 * cdef int _isOpen( self ) * cdef _hasIndex( self ) * cpdef _open(self, mode, loadIndex=*) # <<<<<<<<<<<<<< * cdef char* getrname(self, int tid) * cdef _parseRegion(self, reference=*, start=*, end=*, region=*) */ struct __pyx_opt_args_15samtoolsWrapper_7Samfile__open { int __pyx_n; PyObject *loadIndex; }; /* "samtoolsWrapper.pxd":256 * cpdef _open(self, mode, loadIndex=*) * cdef char* getrname(self, int tid) * cdef _parseRegion(self, reference=*, start=*, end=*, region=*) # <<<<<<<<<<<<<< * cpdef IteratorRow fetch(self, char* reference, int start, int end) * cpdef IteratorRowAll fetchAllReads(self) */ struct __pyx_opt_args_15samtoolsWrapper_7Samfile__parseRegion { int __pyx_n; PyObject *reference; PyObject *start; PyObject *end; PyObject *region; }; /* "samtoolsWrapper.pxd":311 * ################################################################################################### * * ctypedef struct cAlignedRead: # <<<<<<<<<<<<<< * char* seq * char* qual */ struct __pyx_t_15samtoolsWrapper_cAlignedRead { char *seq; char *qual; short *cigarOps; short *hash; short mateChromID; short cigarLen; short chromID; short rlen; int pos; int end; int insertSize; int matePos; int bitFlag; char mapq; }; /* "variant.pxd":42 * ################################################################################################### * * cdef class VariantCandidateGenerator: # <<<<<<<<<<<<<< * cdef int CIGAR_M * cdef int CIGAR_I */ struct __pyx_obj_7variant_VariantCandidateGenerator { PyObject_HEAD struct __pyx_vtabstruct_7variant_VariantCandidateGenerator *__pyx_vtab; int CIGAR_M; int CIGAR_I; int CIGAR_D; int CIGAR_N; int CIGAR_S; int CIGAR_H; int CIGAR_P; int minMapQual; int minBaseQual; int minFlank; int refId; int maxCoverage; int verbosity; int genSNPs; int genIndels; int maxReadLength; long rStart; long rEnd; long refSeqStart; long refSeqEnd; char *refSeq; PyObject *variantHeap; PyObject *pyRefSeq; PyObject *rname; struct __pyx_obj_9fastafile_FastaFile *refFile; PyObject *options; int qualBinSize; }; /* "fastafile.pxd":5 * cdef dict getRefs(self, int parseNCBI) * * cdef class FastaFile(object): # <<<<<<<<<<<<<< * cdef object theFile * cdef FastaIndex theIndex */ struct __pyx_obj_9fastafile_FastaFile { PyObject_HEAD struct __pyx_vtabstruct_9fastafile_FastaFile *__pyx_vtab; PyObject *theFile; struct __pyx_obj_9fastafile_FastaIndex *theIndex; PyObject *refs; PyObject *cache; PyObject *cacheRefName; PY_LONG_LONG cacheStartPos; PY_LONG_LONG cacheEndPos; }; /* "samtoolsWrapper.pxd":266 * ################################################################################################### * * cdef class AlignedRead: # <<<<<<<<<<<<<< * cdef bam1_t* _delegate * cdef int hashValue */ struct __pyx_obj_15samtoolsWrapper_AlignedRead { PyObject_HEAD struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *__pyx_vtab; bam1_t *_delegate; int hashValue; int readEnd; char *_seq; char *_qual; }; /* "samtoolsWrapper.pxd":225 * cdef class Samfile * * cdef class IteratorRow: # <<<<<<<<<<<<<< * cdef bam_fetch_iterator_t* bam_iter # iterator state object * cdef bam1_t* b */ struct __pyx_obj_15samtoolsWrapper_IteratorRow { PyObject_HEAD struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRow *__pyx_vtab; bam_fetch_iterator_t *bam_iter; bam1_t *b; int useIndex; }; /* "samtoolsWrapper.pxd":223 * * ################################################################################################### * cdef class Samfile # <<<<<<<<<<<<<< * * cdef class IteratorRow: */ struct __pyx_obj_15samtoolsWrapper_Samfile { PyObject_HEAD struct __pyx_vtabstruct_15samtoolsWrapper_Samfile *__pyx_vtab; char *filename; samfile_t *samfile; bam_index_t *index; int isbam; PyObject *indexesByRegion; PyObject *lock; }; /* "samtoolsWrapper.pxd":233 * ################################################################################################### * * cdef class IteratorRowAll: # <<<<<<<<<<<<<< * cdef bam1_t* b * cdef samfile_t* fp */ struct __pyx_obj_15samtoolsWrapper_IteratorRowAll { PyObject_HEAD struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRowAll *__pyx_vtab; bam1_t *b; samfile_t *fp; }; /* "fastafile.pxd":1 * cdef class FastaIndex: # <<<<<<<<<<<<<< * cdef object theFile * cdef dict getRefs(self, int parseNCBI) */ struct __pyx_obj_9fastafile_FastaIndex { PyObject_HEAD struct __pyx_vtabstruct_9fastafile_FastaIndex *__pyx_vtab; PyObject *theFile; }; /* "bamfileutils.pxd":22 * ################################################################################################### * * cdef class MultiBamFileReader(object): # <<<<<<<<<<<<<< * cdef public object files * cpdef getRName(self, int refId) */ struct __pyx_obj_12bamfileutils_MultiBamFileReader { PyObject_HEAD struct __pyx_vtabstruct_12bamfileutils_MultiBamFileReader *__pyx_vtab; PyObject *files; }; /* "bamfileutils.pxd":14 * ################################################################################################### * * cdef class MultiBamFileIterator(object): # <<<<<<<<<<<<<< * cdef public list files * cdef list queue */ struct __pyx_obj_12bamfileutils_MultiBamFileIterator { PyObject_HEAD PyObject *files; PyObject *queue; int nReadsInQueue; struct __pyx_obj_15samtoolsWrapper_AlignedRead *lastRead; }; /* "variant.pxd":16 * ################################################################################################### * * cdef class Variant: # <<<<<<<<<<<<<< * cdef: * public bytes refName */ struct __pyx_obj_7variant_Variant { PyObject_HEAD struct __pyx_vtabstruct_7variant_Variant *__pyx_vtab; PyObject *refName; PyObject *added; PyObject *removed; PyObject *bamAdded; PyObject *bamRemoved; int refPos; int bamMinPos; int bamMaxPos; int minRefPos; int maxRefPos; int nSupportingReads; int varSource; int hashValue; int nAdded; int nRemoved; int varType; }; /* "bamfileutils.pxd":7 * ################################################################################################### * * cdef class BamFileIterator(object): # <<<<<<<<<<<<<< * cdef public object iterator * cdef public AlignedRead currentValue */ struct __pyx_obj_12bamfileutils_BamFileIterator { PyObject_HEAD struct __pyx_vtabstruct_12bamfileutils_BamFileIterator *__pyx_vtab; PyObject *iterator; struct __pyx_obj_15samtoolsWrapper_AlignedRead *currentValue; }; /* "fastafile.pxd":1 * cdef class FastaIndex: # <<<<<<<<<<<<<< * cdef object theFile * cdef dict getRefs(self, int parseNCBI) */ struct __pyx_vtabstruct_9fastafile_FastaIndex { PyObject *(*getRefs)(struct __pyx_obj_9fastafile_FastaIndex *, int); }; static struct __pyx_vtabstruct_9fastafile_FastaIndex *__pyx_vtabptr_9fastafile_FastaIndex; /* "samtoolsWrapper.pxd":223 * * ################################################################################################### * cdef class Samfile # <<<<<<<<<<<<<< * * cdef class IteratorRow: */ struct __pyx_vtabstruct_15samtoolsWrapper_Samfile { void (*clearHeader)(struct __pyx_obj_15samtoolsWrapper_Samfile *); void (*clearIndex)(struct __pyx_obj_15samtoolsWrapper_Samfile *); void (*createCache)(struct __pyx_obj_15samtoolsWrapper_Samfile *); void (*clearCache)(struct __pyx_obj_15samtoolsWrapper_Samfile *); int (*_isOpen)(struct __pyx_obj_15samtoolsWrapper_Samfile *); PyObject *(*_hasIndex)(struct __pyx_obj_15samtoolsWrapper_Samfile *); PyObject *(*_open)(struct __pyx_obj_15samtoolsWrapper_Samfile *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_15samtoolsWrapper_7Samfile__open *__pyx_optional_args); char *(*getrname)(struct __pyx_obj_15samtoolsWrapper_Samfile *, int); PyObject *(*_parseRegion)(struct __pyx_obj_15samtoolsWrapper_Samfile *, struct __pyx_opt_args_15samtoolsWrapper_7Samfile__parseRegion *__pyx_optional_args); struct __pyx_obj_15samtoolsWrapper_IteratorRow *(*fetch)(struct __pyx_obj_15samtoolsWrapper_Samfile *, char *, int, int, int __pyx_skip_dispatch); struct __pyx_obj_15samtoolsWrapper_IteratorRowAll *(*fetchAllReads)(struct __pyx_obj_15samtoolsWrapper_Samfile *, int __pyx_skip_dispatch); PyObject *(*close)(struct __pyx_obj_15samtoolsWrapper_Samfile *, int __pyx_skip_dispatch); void (*loadOffsetsForRegions)(struct __pyx_obj_15samtoolsWrapper_Samfile *, PyObject *); void (*openBAMFile)(struct __pyx_obj_15samtoolsWrapper_Samfile *, PyObject *); }; static struct __pyx_vtabstruct_15samtoolsWrapper_Samfile *__pyx_vtabptr_15samtoolsWrapper_Samfile; /* "fastafile.pxd":5 * cdef dict getRefs(self, int parseNCBI) * * cdef class FastaFile(object): # <<<<<<<<<<<<<< * cdef object theFile * cdef FastaIndex theIndex */ struct __pyx_vtabstruct_9fastafile_FastaFile { PyObject *(*getCharacter)(struct __pyx_obj_9fastafile_FastaFile *, PyObject *, PY_LONG_LONG); PyObject *(*getSequence)(struct __pyx_obj_9fastafile_FastaFile *, PyObject *, PY_LONG_LONG, PY_LONG_LONG); void (*setCacheSequence)(struct __pyx_obj_9fastafile_FastaFile *, PyObject *, PY_LONG_LONG, PY_LONG_LONG); }; static struct __pyx_vtabstruct_9fastafile_FastaFile *__pyx_vtabptr_9fastafile_FastaFile; /* "variant.pyx":101 * ################################################################################################### * * cdef class Variant(object): # <<<<<<<<<<<<<< * """ * Class to encapsulate information for all common variant types. The basic */ struct __pyx_vtabstruct_7variant_Variant { double (*indelPrior)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_9fastafile_FastaFile *, int); double (*calculatePrior)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_9fastafile_FastaFile *); void (*addVariant)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_7variant_Variant *); int (*overlaps)(struct __pyx_obj_7variant_Variant *, struct __pyx_obj_7variant_Variant *); }; static struct __pyx_vtabstruct_7variant_Variant *__pyx_vtabptr_7variant_Variant; /* "samtoolsWrapper.pxd":233 * ################################################################################################### * * cdef class IteratorRowAll: # <<<<<<<<<<<<<< * cdef bam1_t* b * cdef samfile_t* fp */ struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRowAll { bam1_t *(*getCurrent)(struct __pyx_obj_15samtoolsWrapper_IteratorRowAll *); int (*cnext)(struct __pyx_obj_15samtoolsWrapper_IteratorRowAll *); }; static struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRowAll *__pyx_vtabptr_15samtoolsWrapper_IteratorRowAll; /* "bamfileutils.pxd":22 * ################################################################################################### * * cdef class MultiBamFileReader(object): # <<<<<<<<<<<<<< * cdef public object files * cpdef getRName(self, int refId) */ struct __pyx_vtabstruct_12bamfileutils_MultiBamFileReader { PyObject *(*getRName)(struct __pyx_obj_12bamfileutils_MultiBamFileReader *, int, int __pyx_skip_dispatch); struct __pyx_obj_12bamfileutils_MultiBamFileIterator *(*fetch)(struct __pyx_obj_12bamfileutils_MultiBamFileReader *, char *, int, int, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_12bamfileutils_MultiBamFileReader *__pyx_vtabptr_12bamfileutils_MultiBamFileReader; /* "samtoolsWrapper.pxd":266 * ################################################################################################### * * cdef class AlignedRead: # <<<<<<<<<<<<<< * cdef bam1_t* _delegate * cdef int hashValue */ struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead { PyObject *(*qname)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *, int __pyx_skip_dispatch); char *(*fastQName)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); char *(*seq)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); char *(*qual)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); PyObject *(*tags)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*flag)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*rname)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*getCigarLength)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*pos)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*end)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); PyObject *(*bin)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*getCigarOpCode)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *, int); int (*getCigarOpLength)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *, int); int (*rlen)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*mapq)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *, int __pyx_skip_dispatch); int (*mrnm)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*mpos)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*isize)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_paired)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_proper_pair)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_unmapped)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*mate_is_unmapped)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_reverse)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*mate_is_reverse)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_read1)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_read2)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_secondary)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_qcfail)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); int (*is_duplicate)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *); PyObject *(*opt)(struct __pyx_obj_15samtoolsWrapper_AlignedRead *, PyObject *); }; static struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *__pyx_vtabptr_15samtoolsWrapper_AlignedRead; /* "variant.pyx":472 * ################################################################################################### * * cdef class VariantCandidateGenerator(object): # <<<<<<<<<<<<<< * """ * A class to generate variant candidates from a bunch of reads. */ struct __pyx_vtabstruct_7variant_VariantCandidateGenerator { void (*addVariantToList)(struct __pyx_obj_7variant_VariantCandidateGenerator *, struct __pyx_obj_7variant_Variant *); void (*getSnpCandidatesFromReadSegment)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_15samtoolsWrapper_cAlignedRead *, char *, char *, int, int, int, int, int); void (*getVariantCandidatesFromSingleRead)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_15samtoolsWrapper_cAlignedRead *); void (*addCandidatesFromReads)(struct __pyx_obj_7variant_VariantCandidateGenerator *, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **); PyObject *(*getCandidates)(struct __pyx_obj_7variant_VariantCandidateGenerator *, int); PyObject *(*getListOfSnpPositions)(struct __pyx_obj_7variant_VariantCandidateGenerator *, struct __pyx_obj_15samtoolsWrapper_AlignedRead *); PyObject *(*getListOfIndelPositions)(struct __pyx_obj_7variant_VariantCandidateGenerator *, struct __pyx_obj_15samtoolsWrapper_AlignedRead *); }; static struct __pyx_vtabstruct_7variant_VariantCandidateGenerator *__pyx_vtabptr_7variant_VariantCandidateGenerator; /* "bamfileutils.pxd":7 * ################################################################################################### * * cdef class BamFileIterator(object): # <<<<<<<<<<<<<< * cdef public object iterator * cdef public AlignedRead currentValue */ struct __pyx_vtabstruct_12bamfileutils_BamFileIterator { PyObject *(*next)(struct __pyx_obj_12bamfileutils_BamFileIterator *, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_12bamfileutils_BamFileIterator *__pyx_vtabptr_12bamfileutils_BamFileIterator; /* "samtoolsWrapper.pxd":225 * cdef class Samfile * * cdef class IteratorRow: # <<<<<<<<<<<<<< * cdef bam_fetch_iterator_t* bam_iter # iterator state object * cdef bam1_t* b */ struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRow { int (*cnext)(struct __pyx_obj_15samtoolsWrapper_IteratorRow *); 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/*proto*/ /* Module declarations from 'cython' */ /* Module declarations from 'bamfileutils' */ static PyTypeObject *__pyx_ptype_12bamfileutils_BamFileIterator = 0; static PyTypeObject *__pyx_ptype_12bamfileutils_MultiBamFileIterator = 0; static PyTypeObject *__pyx_ptype_12bamfileutils_MultiBamFileReader = 0; /* Module declarations from 'cerrormodel' */ static PyObject *(*__pyx_f_11cerrormodel_calculate_size_and_displacement)(PyObject *, char); /*proto*/ /* Module declarations from 'variant' */ static PyTypeObject *__pyx_ptype_7variant_Variant = 0; static PyTypeObject *__pyx_ptype_7variant_VariantCandidateGenerator = 0; __PYX_EXTERN_C DL_EXPORT(int) PLATYPUS_VAR; __PYX_EXTERN_C DL_EXPORT(int) FILE_VAR; __PYX_EXTERN_C DL_EXPORT(int) ASSEMBLER_VAR; static double __pyx_v_7variant_mLTOT; static int __pyx_v_7variant_SNP; static int __pyx_v_7variant_MNP; static int __pyx_v_7variant_INS; static int __pyx_v_7variant_DEL; static int __pyx_v_7variant_REP; static PyObject *__pyx_v_7variant_varTypes = 0; static PyObject *__pyx_v_7variant_indel_prior_model = 0; static double __pyx_v_7variant_complex_deletion_prior; static double __pyx_v_7variant_complex_insertion_prior; #define __Pyx_MODULE_NAME "variant" int __pyx_module_is_main_variant = 0; /* Implementation of 'variant' */ static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_sorted; static int __pyx_pf_7variant_7Variant___init__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_refName, int __pyx_v_refPos, char *__pyx_v_removed, char *__pyx_v_added, int __pyx_v_nSupportingReads, int __pyx_v_varSource); /* proto */ static Py_hash_t __pyx_pf_7variant_7Variant_2__hash__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_4__richcmp__(struct __pyx_obj_7variant_Variant *__pyx_v_self, struct __pyx_obj_7variant_Variant *__pyx_v_other, int __pyx_v_opCode); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_6__str__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_8__repr__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_10shortRepr(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_7refName___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_7refName_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_7variant_7Variant_7refName_4__del__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_5added___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_5added_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_7variant_7Variant_5added_4__del__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_7removed___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_7removed_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_7variant_7Variant_7removed_4__del__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_8bamAdded___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_8bamAdded_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_7variant_7Variant_8bamAdded_4__del__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_10bamRemoved___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_10bamRemoved_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_7variant_7Variant_10bamRemoved_4__del__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_6refPos___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_6refPos_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_9bamMinPos___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_9bamMinPos_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_9bamMaxPos___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_9bamMaxPos_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_9minRefPos___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_9minRefPos_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_9maxRefPos___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_9maxRefPos_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_16nSupportingReads___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_16nSupportingReads_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_9varSource___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_9varSource_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_9hashValue___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_9hashValue_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_6nAdded___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_6nAdded_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_8nRemoved___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_8nRemoved_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_7variant_7Variant_7varType___get__(struct __pyx_obj_7variant_Variant *__pyx_v_self); /* proto */ static int __pyx_pf_7variant_7Variant_7varType_2__set__(struct __pyx_obj_7variant_Variant *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_7variant_25VariantCandidateGenerator___init__(struct __pyx_obj_7variant_VariantCandidateGenerator *__pyx_v_self, PyObject *__pyx_v_region, struct __pyx_obj_9fastafile_FastaFile *__pyx_v_referenceFile, int __pyx_v_minMapQual, int __pyx_v_minFlank, int __pyx_v_minBaseQual, int __pyx_v_maxCoverage, int __pyx_v_maxReadLength, PyObject *__pyx_v_options, int __pyx_v_verbosity, int __pyx_v_genSNPs, int __pyx_v_genIndels); /* proto */ static char __pyx_k_1[] = ""; static char __pyx_k_2[] = "%s(%s:%s-%s"; static char __pyx_k_3[] = " -"; static char __pyx_k_4[] = " +"; static char __pyx_k_5[] = " nReads = %s, Source= %s"; static char __pyx_k_6[] = ")"; static char __pyx_k_7[] = "Adding new variant %s to candidate list"; static char __pyx_k_8[] = "Adding variant %s to existing variant in candidate list"; static char __pyx_k_9[] = "Something is very wrong. Base qual is %s"; static char __pyx_k_10[] = "Splitting long mis-match into two variants at %s."; static char __pyx_k_13[] = "\nUtility module, containing classes to handle reading and writing\nfiles of variants.\n"; static char __pyx_k_15[] = "LIGC@:62/-*'&%$"; static char __pyx_k_16[] = "LIGDB@><9630.,+**)(''&&%%%$$$"; static char __pyx_k_17[] = "LIGA@B@><;8763220/.-,+++)*))(((''''&&&&&&%%%%%%%%$$$$$$$"; static char __pyx_k_18[] = "LIGA@\077\077?=<886533210/.--,+**))))((('''''&&&&&&&&%%%%%%%%%%%$$$$$$$$"; static char __pyx_k_19[] = "LIGA@\077\077>=>=;966543210///-,,++*"; static char __pyx_k_20[] = "LIGA@\077\077>>=<=;:764532210/----,++"; static char __pyx_k_21[] = "LIGA@\077\077>>==<;;987543210/....-,,,++++"; static char __pyx_k_22[] = "LIGA@\077\077>>==<<;9876432200/..--,,,+++"; static char __pyx_k_23[] = "LIGA@\077\077>>==<<;;9966432100//../..----,,,,,++++++"; static char __pyx_k_24[] = "LIGA@\077\077>>==<<;;:986432110//..----,,,,++++"; static char __pyx_k_25[] = "LIGA@\077\077>>==<<<;;:87642210////..--,,,,,+++"; static char __pyx_k_26[] = "LIGA@\077\077>>==<<<;;;:986532110000/...-----,,,,,+++++"; static char __pyx_k_27[] = "LIGA@\077\077>>==<<<;;;::987543111000/////.......--------,,,,,,,,,,,,,+++++++++"; static char __pyx_k_28[] = "LIGA@\077\077>>==<<<;;;::987642210/0/.....-------,,,,,,,,+++++++"; static char __pyx_k_29[] = "LIGA@\077\077>>==<<<;;;;::988754322110000////////.......------------,,,,,,,,,,,,,,,,,++++++++++"; static char __pyx_k_30[] = "LIGA@\077\077>>==<<<;;;;:::98765321110////........-------,,,,,,,,,,,,,,+++++++++"; static char __pyx_k_31[] = "LIGA@\077\077>>==<<<;;;;::::988764433211110000000///////.............-----------------,,,,,,,,,,,,,,,,,,,"; static char __pyx_k_32[] = "LIGA@\077\077>>==<<<;;;:::::998875433221111000000///////.............-----------------,,,,,,,,,,,,,,,,,,,"; static char __pyx_k_33[] = "LIGA@\077\077>>==<<<;;;;::::999887654433222221111111100000000//////////////..................------------"; static char __pyx_k_34[] = "LIGA@\077\077>>==<<<;;;;::::9999876543322111000000///////............-----------------,,,,,,,,,,,,,,,,,,,"; static char __pyx_k_35[] = "LIGA@\077\077>>==<<<;;;;::::9999988765544433322222221111111100000000000000//////////////////............."; static char __pyx_k_36[] = "LIGA@\077\077>>==<<<;;;;::::9999987765432221000000////////...........-----------------,,,,,,,,,,,,,,,,,,,"; static char __pyx_k_37[] = "LIGA@\077\077>>==<<<;;;;::::9999998776543322111100000000////////................-------------------,,,,,,"; static char __pyx_k_38[] = "LIGA@\077\077>>==<<<;;;;::::9999998887654433322111111100000000/////////////...................-----------"; static char __pyx_k__N[] = "N"; static char __pyx_k__DEL[] = "DEL"; static char __pyx_k__INS[] = "INS"; static char __pyx_k__Log[] = "Log"; static char __pyx_k__MNP[] = "MNP"; static char __pyx_k__REP[] = "REP"; static char __pyx_k__SNP[] = "SNP"; static char __pyx_k__pow[] = "pow"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__math[] = "math"; static char __pyx_k__added[] = "added"; static char __pyx_k__count[] = "count"; static char __pyx_k__debug[] = "debug"; static char __pyx_k__range[] = "range"; static char __pyx_k__logger[] = "logger"; static char __pyx_k__refPos[] = "refPos"; static char __pyx_k__region[] = "region"; static char __pyx_k__sorted[] = "sorted"; static char __pyx_k__genSNPs[] = "genSNPs"; static char __pyx_k__logging[] = "logging"; static char __pyx_k__options[] = "options"; static char __pyx_k__refName[] = "refName"; static char __pyx_k__removed[] = "removed"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__datetime[] = "datetime"; static char __pyx_k__minFlank[] = "minFlank"; static char __pyx_k__SeqLength[] = "SeqLength"; static char __pyx_k__fastafile[] = "fastafile"; static char __pyx_k__genIndels[] = "genIndels"; static char __pyx_k__getLogger[] = "getLogger"; static char __pyx_k__varSource[] = "varSource"; static char __pyx_k__verbosity[] = "verbosity"; static char __pyx_k__IndexError[] = "IndexError"; static char __pyx_k__minMapQual[] = "minMapQual"; static char __pyx_k__maxCoverage[] = "maxCoverage"; static char __pyx_k__minBaseQual[] = "minBaseQual"; static char __pyx_k__qualBinSize[] = "qualBinSize"; static char __pyx_k__maxReadLength[] = "maxReadLength"; static char __pyx_k__referenceFile[] = "referenceFile"; static char __pyx_k__samtoolsWrapper[] = "samtoolsWrapper"; static char __pyx_k__nSupportingReads[] = "nSupportingReads"; static PyObject *__pyx_kp_s_1; static PyObject *__pyx_kp_s_10; static PyObject *__pyx_kp_s_15; static PyObject *__pyx_kp_s_16; static PyObject *__pyx_kp_s_17; static PyObject *__pyx_kp_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_2; static PyObject *__pyx_kp_s_20; static PyObject *__pyx_kp_s_21; static PyObject *__pyx_kp_s_22; static PyObject *__pyx_kp_s_23; static PyObject *__pyx_kp_s_24; static PyObject *__pyx_kp_s_25; static PyObject *__pyx_kp_s_26; static PyObject *__pyx_kp_s_27; static PyObject *__pyx_kp_s_28; static PyObject *__pyx_kp_s_29; static PyObject *__pyx_kp_s_3; static PyObject *__pyx_kp_s_30; static PyObject *__pyx_kp_s_31; static PyObject *__pyx_kp_s_32; static PyObject *__pyx_kp_s_33; static PyObject *__pyx_kp_s_34; static PyObject *__pyx_kp_s_35; static PyObject *__pyx_kp_s_36; static PyObject *__pyx_kp_s_37; static PyObject *__pyx_kp_s_38; static PyObject *__pyx_kp_s_4; static PyObject *__pyx_kp_s_5; static PyObject *__pyx_kp_s_6; static PyObject *__pyx_kp_s_7; static PyObject *__pyx_kp_s_8; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_n_s__DEL; static PyObject *__pyx_n_s__INS; static PyObject *__pyx_n_s__IndexError; static PyObject *__pyx_n_s__Log; static PyObject *__pyx_n_s__MNP; static PyObject *__pyx_n_s__N; static PyObject *__pyx_n_s__REP; static PyObject *__pyx_n_s__SNP; static PyObject *__pyx_n_s__SeqLength; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s__added; static PyObject *__pyx_n_s__count; static PyObject *__pyx_n_s__datetime; static PyObject *__pyx_n_s__debug; static PyObject *__pyx_n_s__fastafile; static PyObject *__pyx_n_s__genIndels; static PyObject *__pyx_n_s__genSNPs; static PyObject *__pyx_n_s__getLogger; static PyObject *__pyx_n_s__logger; static PyObject *__pyx_n_s__logging; static PyObject *__pyx_n_s__math; static PyObject *__pyx_n_s__maxCoverage; static PyObject *__pyx_n_s__maxReadLength; static PyObject *__pyx_n_s__minBaseQual; static PyObject *__pyx_n_s__minFlank; static PyObject *__pyx_n_s__minMapQual; static PyObject *__pyx_n_s__nSupportingReads; static PyObject *__pyx_n_s__options; static PyObject *__pyx_n_s__pow; static PyObject *__pyx_n_s__qualBinSize; static PyObject *__pyx_n_s__range; static PyObject *__pyx_n_s__refName; static PyObject *__pyx_n_s__refPos; static PyObject *__pyx_n_s__referenceFile; static PyObject *__pyx_n_s__region; static PyObject *__pyx_n_s__removed; static PyObject *__pyx_n_s__samtoolsWrapper; static PyObject *__pyx_n_s__sorted; static PyObject *__pyx_n_s__varSource; static PyObject *__pyx_n_s__verbosity; static PyObject *__pyx_n_s__zip; static PyObject *__pyx_int_0; static PyObject *__pyx_int_1; static PyObject *__pyx_int_2; static PyObject *__pyx_int_3; static PyObject *__pyx_int_4; static PyObject *__pyx_int_5; static PyObject *__pyx_int_6; static PyObject *__pyx_int_7; static PyObject *__pyx_int_8; static PyObject *__pyx_int_9; static PyObject *__pyx_int_10; static PyObject *__pyx_int_11; static PyObject *__pyx_int_12; static PyObject *__pyx_int_13; static PyObject *__pyx_int_14; static PyObject *__pyx_int_15; static PyObject *__pyx_int_16; static PyObject *__pyx_int_17; static PyObject *__pyx_int_18; static PyObject *__pyx_int_19; static PyObject *__pyx_int_20; static PyObject *__pyx_int_21; static PyObject *__pyx_int_22; static PyObject *__pyx_int_23; static PyObject *__pyx_int_24; static PyObject *__pyx_int_100; static PyObject *__pyx_int_2000; static PyObject *__pyx_k_tuple_11; static PyObject *__pyx_k_tuple_12; static PyObject *__pyx_k_tuple_14; int PLATYPUS_VAR; int FILE_VAR; int ASSEMBLER_VAR; /* Python wrapper */ static int __pyx_pw_7variant_7Variant_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static char __pyx_doc_7variant_7Variant___init__[] = "\n Constructor. Takes the name of the reference sequence (e.g. 'chr1'),\n the position of the variant (given by the left-most co-ordinate of the\n changed sequence (so a SNP co-ordinate is the exact location of the SNP,\n an indel co-ordinate is the location of the first inserted base, and a deletion\n co-ordinate is the location of the first deleted base)), the removed and added\n sequences, and the supporting read.\n "; #if CYTHON_COMPILING_IN_CPYTHON struct wrapperbase __pyx_wrapperbase_7variant_7Variant___init__; #endif static int __pyx_pw_7variant_7Variant_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_refName = 0; int __pyx_v_refPos; char *__pyx_v_removed; char *__pyx_v_added; int __pyx_v_nSupportingReads; int __pyx_v_varSource; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__refName,&__pyx_n_s__refPos,&__pyx_n_s__removed,&__pyx_n_s__added,&__pyx_n_s__nSupportingReads,&__pyx_n_s__varSource,0}; PyObject* values[6] = {0,0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__refName)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__refPos)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__removed)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__added)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__nSupportingReads)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__varSource)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; 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/* "variant.pyx":544 * cdef int baseQual = 0 * cdef int readIndex = 0 * cdef int refIndex = 0 # <<<<<<<<<<<<<< * cdef char readChar * cdef char refChar */ __pyx_v_refIndex = 0; /* "variant.pyx":551 * cdef bytes mSNPRead * * cdef int misMatchStartRef = -1 # <<<<<<<<<<<<<< * cdef int misMatchEndRef = -1 * cdef int misMatchStartRead = -1 */ __pyx_v_misMatchStartRef = -1; /* "variant.pyx":552 * * cdef int misMatchStartRef = -1 * cdef int misMatchEndRef = -1 # <<<<<<<<<<<<<< * cdef int misMatchStartRead = -1 * cdef int misMatchEndRead = -1 */ __pyx_v_misMatchEndRef = -1; /* "variant.pyx":553 * cdef int misMatchStartRef = -1 * cdef int misMatchEndRef = -1 * cdef int misMatchStartRead = -1 # <<<<<<<<<<<<<< * cdef int misMatchEndRead = -1 * */ __pyx_v_misMatchStartRead = -1; /* "variant.pyx":554 * cdef int misMatchEndRef = -1 * cdef int misMatchStartRead = -1 * cdef int misMatchEndRead = -1 # <<<<<<<<<<<<<< * * for index from 0 <= index < lenSeqToCheck: */ __pyx_v_misMatchEndRead = -1; /* "variant.pyx":556 * cdef int misMatchEndRead = -1 * * for index from 0 <= index < lenSeqToCheck: # <<<<<<<<<<<<<< * * # Don't look at the first 'minFlank' bases for candidate generation */ __pyx_t_1 = __pyx_v_lenSeqToCheck; 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Base qual is %s" %(baseQual) # <<<<<<<<<<<<<< * * if readChar != refChar: */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!(__pyx_v_baseQual <= 93))) { __pyx_t_6 = PyInt_FromLong(__pyx_v_baseQual); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_5)); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_5)); __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #endif /* "variant.pyx":578 * assert baseQual <= 93, "Something is very wrong. 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Added = %s. removed = %s. pos = %s" %(mSNPRead, mSNPRef, misMatchStartRef + self.refSeqStart)) */ __pyx_t_8 = PyBytes_FromStringAndSize(((const char*)__pyx_v_self->refSeq) + __pyx_v_misMatchStartRef, (__pyx_v_misMatchEndRef + 1) - __pyx_v_misMatchStartRef); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __Pyx_XDECREF(((PyObject *)__pyx_v_mSNPRef)); __pyx_v_mSNPRef = __pyx_t_8; __pyx_t_8 = 0; /* "variant.pyx":598 * * mSNPRef = self.refSeq[misMatchStartRef: misMatchEndRef+1] * mSNPRead = readSeq[misMatchStartRead: misMatchEndRead+1] # <<<<<<<<<<<<<< * #logger.info("Adding MNP. 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/* "variant.pyx":744 * """ * cdef int readStart = read.pos() * cdef int flag = 0 # <<<<<<<<<<<<<< * cdef int length = 0 * cdef int refOffset = 0 */ __pyx_v_flag = 0; /* "variant.pyx":745 * cdef int readStart = read.pos() * cdef int flag = 0 * cdef int length = 0 # <<<<<<<<<<<<<< * cdef int refOffset = 0 * cdef int readOffset = 0 */ __pyx_v_length = 0; /* "variant.pyx":746 * cdef int flag = 0 * cdef int length = 0 * cdef int refOffset = 0 # <<<<<<<<<<<<<< * cdef int readOffset = 0 * cdef int cigarIndex = 0 */ __pyx_v_refOffset = 0; /* "variant.pyx":747 * cdef int length = 0 * cdef int refOffset = 0 * cdef int readOffset = 0 # <<<<<<<<<<<<<< * cdef int cigarIndex = 0 * cdef int cigarLength = read.getCigarLength() */ __pyx_v_readOffset = 0; /* "variant.pyx":748 * cdef int refOffset = 0 * cdef int readOffset = 0 * cdef int cigarIndex = 0 # <<<<<<<<<<<<<< * cdef int cigarLength = read.getCigarLength() * cdef int index = 0 */ __pyx_v_cigarIndex = 0; /* "variant.pyx":749 * cdef int readOffset = 0 * cdef int cigarIndex = 0 * cdef int cigarLength = read.getCigarLength() # <<<<<<<<<<<<<< * cdef int index = 0 * cdef int baseQual = 0 */ __pyx_v_cigarLength = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->getCigarLength(__pyx_v_read); /* "variant.pyx":750 * cdef int cigarIndex = 0 * cdef int cigarLength = read.getCigarLength() * cdef int index = 0 # <<<<<<<<<<<<<< * cdef int baseQual = 0 * cdef int readIndex = 0 */ __pyx_v_index = 0; /* "variant.pyx":751 * cdef int cigarLength = read.getCigarLength() * cdef int index = 0 * cdef int baseQual = 0 # <<<<<<<<<<<<<< * cdef int readIndex = 0 * cdef int refIndex = 0 */ __pyx_v_baseQual = 0; /* "variant.pyx":752 * cdef int index = 0 * cdef int baseQual = 0 * cdef int readIndex = 0 # <<<<<<<<<<<<<< * cdef int refIndex = 0 * cdef int readLength = read.rlen() */ __pyx_v_readIndex = 0; /* "variant.pyx":753 * cdef int baseQual = 0 * cdef int readIndex = 0 * cdef int refIndex = 0 # <<<<<<<<<<<<<< * cdef int readLength = read.rlen() * cdef int isReverse = read.is_reverse() */ __pyx_v_refIndex = 0; /* "variant.pyx":754 * cdef int readIndex = 0 * cdef int refIndex = 0 * cdef int readLength = read.rlen() # <<<<<<<<<<<<<< * cdef int isReverse = read.is_reverse() * cdef char* readQual = read.qual() */ __pyx_v_readLength = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->rlen(__pyx_v_read); /* "variant.pyx":755 * cdef int refIndex = 0 * cdef int readLength = read.rlen() * cdef int isReverse = read.is_reverse() # <<<<<<<<<<<<<< * cdef char* readQual = read.qual() * cdef char* readSeq = read.seq() */ __pyx_v_isReverse = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->is_reverse(__pyx_v_read); /* "variant.pyx":756 * cdef int readLength = read.rlen() * cdef int isReverse = read.is_reverse() * cdef char* readQual = read.qual() # <<<<<<<<<<<<<< * cdef char* readSeq = read.seq() * cdef char readChar */ __pyx_v_readQual = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->qual(__pyx_v_read); /* "variant.pyx":757 * cdef int isReverse = read.is_reverse() * cdef char* readQual = read.qual() * cdef char* readSeq = read.seq() # <<<<<<<<<<<<<< * cdef char readChar * cdef char refChar */ __pyx_v_readSeq = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->seq(__pyx_v_read); /* "variant.pyx":760 * cdef char readChar * cdef char refChar * cdef list snpPos = [] # <<<<<<<<<<<<<< * * for cigarIndex from 0 <= cigarIndex < cigarLength: */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_snpPos = __pyx_t_1; __pyx_t_1 = 0; /* "variant.pyx":762 * cdef list snpPos = [] * * for cigarIndex from 0 <= cigarIndex < cigarLength: # <<<<<<<<<<<<<< * * flag = read.getCigarOpCode(cigarIndex) */ __pyx_t_2 = __pyx_v_cigarLength; for (__pyx_v_cigarIndex = 0; __pyx_v_cigarIndex < __pyx_t_2; __pyx_v_cigarIndex++) { /* "variant.pyx":764 * for cigarIndex from 0 <= cigarIndex < cigarLength: * * flag = read.getCigarOpCode(cigarIndex) # <<<<<<<<<<<<<< * length = read.getCigarOpLength(cigarIndex) * */ __pyx_v_flag = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->getCigarOpCode(__pyx_v_read, __pyx_v_cigarIndex); /* "variant.pyx":765 * * flag = read.getCigarOpCode(cigarIndex) * length = read.getCigarOpLength(cigarIndex) # <<<<<<<<<<<<<< * * # An insertion take us further along the read, but not the reference */ __pyx_v_length = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->getCigarOpLength(__pyx_v_read, __pyx_v_cigarIndex); /* "variant.pyx":768 * * # An insertion take us further along the read, but not the reference * if flag == self.CIGAR_I: # <<<<<<<<<<<<<< * readOffset += length * */ __pyx_t_3 = (__pyx_v_flag == __pyx_v_self->CIGAR_I); if (__pyx_t_3) { /* "variant.pyx":769 * # An insertion take us further along the read, but not the reference * if flag == self.CIGAR_I: * readOffset += length # <<<<<<<<<<<<<< * * # A deletion take us further along the reference, but not the read */ __pyx_v_readOffset = (__pyx_v_readOffset + __pyx_v_length); goto __pyx_L5; } /* "variant.pyx":772 * * # A deletion take us further along the reference, but not the read * elif flag == self.CIGAR_D: # <<<<<<<<<<<<<< * refOffset += length * */ __pyx_t_3 = (__pyx_v_flag == __pyx_v_self->CIGAR_D); if (__pyx_t_3) { /* "variant.pyx":773 * # A deletion take us further along the reference, but not the read * elif flag == self.CIGAR_D: * refOffset += length # <<<<<<<<<<<<<< * * # A match take us further along the reference and the read */ __pyx_v_refOffset = (__pyx_v_refOffset + __pyx_v_length); goto __pyx_L5; } /* "variant.pyx":776 * * # A match take us further along the reference and the read * elif flag == self.CIGAR_M: # <<<<<<<<<<<<<< * * for index from 0 <= index < length: */ __pyx_t_3 = (__pyx_v_flag == __pyx_v_self->CIGAR_M); if (__pyx_t_3) { /* "variant.pyx":778 * elif flag == self.CIGAR_M: * * for index from 0 <= index < length: # <<<<<<<<<<<<<< * * readIndex = index + readOffset */ __pyx_t_4 = __pyx_v_length; for (__pyx_v_index = 0; __pyx_v_index < __pyx_t_4; __pyx_v_index++) { /* "variant.pyx":780 * for index from 0 <= index < length: * * readIndex = index + readOffset # <<<<<<<<<<<<<< * refIndex = (index + refOffset + readStart) - self.refSeqStart * readChar = readSeq[readIndex] */ __pyx_v_readIndex = (__pyx_v_index + __pyx_v_readOffset); /* "variant.pyx":781 * * readIndex = index + readOffset * refIndex = (index + refOffset + readStart) - self.refSeqStart # <<<<<<<<<<<<<< * readChar = readSeq[readIndex] * refChar = self.refSeq[refIndex] */ __pyx_v_refIndex = (((__pyx_v_index + __pyx_v_refOffset) + __pyx_v_readStart) - __pyx_v_self->refSeqStart); /* "variant.pyx":782 * readIndex = index + readOffset * refIndex = (index + refOffset + readStart) - self.refSeqStart * readChar = readSeq[readIndex] # <<<<<<<<<<<<<< * refChar = self.refSeq[refIndex] * baseQual = readQual[readIndex] */ __pyx_v_readChar = (__pyx_v_readSeq[__pyx_v_readIndex]); /* "variant.pyx":783 * refIndex = (index + refOffset + readStart) - self.refSeqStart * readChar = readSeq[readIndex] * refChar = self.refSeq[refIndex] # <<<<<<<<<<<<<< * baseQual = readQual[readIndex] * */ __pyx_v_refChar = (__pyx_v_self->refSeq[__pyx_v_refIndex]); /* "variant.pyx":784 * readChar = readSeq[readIndex] * refChar = self.refSeq[refIndex] * baseQual = readQual[readIndex] # <<<<<<<<<<<<<< * * if readChar != refChar and readChar != 'N' and refChar != 'N' and baseQual >= self.minBaseQual: */ __pyx_v_baseQual = (__pyx_v_readQual[__pyx_v_readIndex]); /* "variant.pyx":786 * baseQual = readQual[readIndex] * * if readChar != refChar and readChar != 'N' and refChar != 'N' and baseQual >= self.minBaseQual: # <<<<<<<<<<<<<< * if isReverse: * snpPos.append(readLength - readIndex - 1) */ __pyx_t_3 = (__pyx_v_readChar != __pyx_v_refChar); if (__pyx_t_3) { __pyx_t_5 = (__pyx_v_readChar != 'N'); if (__pyx_t_5) { __pyx_t_6 = (__pyx_v_refChar != 'N'); if (__pyx_t_6) { __pyx_t_7 = (__pyx_v_baseQual >= __pyx_v_self->minBaseQual); __pyx_t_8 = __pyx_t_7; } else { __pyx_t_8 = __pyx_t_6; } __pyx_t_6 = __pyx_t_8; } else { __pyx_t_6 = __pyx_t_5; } __pyx_t_5 = __pyx_t_6; } else { __pyx_t_5 = __pyx_t_3; } if (__pyx_t_5) { /* "variant.pyx":787 * * if readChar != refChar and readChar != 'N' and refChar != 'N' and baseQual >= self.minBaseQual: * if isReverse: # <<<<<<<<<<<<<< * snpPos.append(readLength - readIndex - 1) * else: */ if (__pyx_v_isReverse) { /* "variant.pyx":788 * if readChar != refChar and readChar != 'N' and refChar != 'N' and baseQual >= self.minBaseQual: * if isReverse: * snpPos.append(readLength - readIndex - 1) # <<<<<<<<<<<<<< * else: * snpPos.append(readIndex) */ __pyx_t_1 = PyInt_FromLong(((__pyx_v_readLength - __pyx_v_readIndex) - 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_9 = PyList_Append(__pyx_v_snpPos, __pyx_t_1); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L9; } /*else*/ { /* "variant.pyx":790 * snpPos.append(readLength - readIndex - 1) * else: * snpPos.append(readIndex) # <<<<<<<<<<<<<< * * readOffset += length */ __pyx_t_1 = PyInt_FromLong(__pyx_v_readIndex); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_9 = PyList_Append(__pyx_v_snpPos, __pyx_t_1); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } __pyx_L9:; goto __pyx_L8; } __pyx_L8:; } /* "variant.pyx":792 * snpPos.append(readIndex) * * readOffset += length # <<<<<<<<<<<<<< * refOffset += length * */ __pyx_v_readOffset = (__pyx_v_readOffset + __pyx_v_length); /* "variant.pyx":793 * * readOffset += length * refOffset += length # <<<<<<<<<<<<<< * * # Other kinds of CIGAR flag. Most likely padding information (MAQ uses this). */ __pyx_v_refOffset = (__pyx_v_refOffset + __pyx_v_length); goto __pyx_L5; } /*else*/ { /* "variant.pyx":797 * # Other kinds of CIGAR flag. Most likely padding information (MAQ uses this). * else: * continue # <<<<<<<<<<<<<< * * if isReverse: */ goto __pyx_L3_continue; } __pyx_L5:; __pyx_L3_continue:; } /* "variant.pyx":799 * continue * * if isReverse: # <<<<<<<<<<<<<< * snpPos.reverse() * return snpPos */ if (__pyx_v_isReverse) { /* "variant.pyx":800 * * if isReverse: * snpPos.reverse() # <<<<<<<<<<<<<< * return snpPos * */ __pyx_t_9 = PyList_Reverse(__pyx_v_snpPos); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L10; } __pyx_L10:; /* "variant.pyx":801 * if isReverse: * snpPos.reverse() * return snpPos # <<<<<<<<<<<<<< * * cdef list getListOfIndelPositions(self, AlignedRead read): */ __Pyx_XDECREF(((PyObject *)__pyx_r)); __Pyx_INCREF(((PyObject *)__pyx_v_snpPos)); __pyx_r = __pyx_v_snpPos; goto __pyx_L0; __pyx_r = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("variant.VariantCandidateGenerator.getListOfSnpPositions", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XDECREF(__pyx_v_snpPos); __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "variant.pyx":803 * return snpPos * * cdef list getListOfIndelPositions(self, AlignedRead read): # <<<<<<<<<<<<<< * """ * Return a list of positions at which the read has indel candidates. */ static PyObject *__pyx_f_7variant_25VariantCandidateGenerator_getListOfIndelPositions(struct __pyx_obj_7variant_VariantCandidateGenerator *__pyx_v_self, struct __pyx_obj_15samtoolsWrapper_AlignedRead *__pyx_v_read) { CYTHON_UNUSED int __pyx_v_readStart; int __pyx_v_flag; int __pyx_v_length; int __pyx_v_refOffset; int __pyx_v_readOffset; int __pyx_v_cigarIndex; int __pyx_v_cigarLength; CYTHON_UNUSED int __pyx_v_index; CYTHON_UNUSED int __pyx_v_baseQual; CYTHON_UNUSED int __pyx_v_readIndex; CYTHON_UNUSED int __pyx_v_refIndex; int __pyx_v_readLength; int __pyx_v_isReverse; CYTHON_UNUSED char *__pyx_v_readQual; CYTHON_UNUSED char *__pyx_v_readSeq; PyObject *__pyx_v_indelPos = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("getListOfIndelPositions", 0); /* "variant.pyx":807 * Return a list of positions at which the read has indel candidates. * """ * cdef int readStart = read.pos() # <<<<<<<<<<<<<< * cdef int flag = 0 * cdef int length = 0 */ __pyx_v_readStart = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->pos(__pyx_v_read); /* "variant.pyx":808 * """ * cdef int readStart = read.pos() * cdef int flag = 0 # <<<<<<<<<<<<<< * cdef int length = 0 * cdef int refOffset = 0 */ __pyx_v_flag = 0; /* "variant.pyx":809 * cdef int readStart = read.pos() * cdef int flag = 0 * cdef int length = 0 # <<<<<<<<<<<<<< * cdef int refOffset = 0 * cdef int readOffset = 0 */ __pyx_v_length = 0; /* "variant.pyx":810 * cdef int flag = 0 * cdef int length = 0 * cdef int refOffset = 0 # <<<<<<<<<<<<<< * cdef int readOffset = 0 * cdef int cigarIndex = 0 */ __pyx_v_refOffset = 0; /* "variant.pyx":811 * cdef int length = 0 * cdef int refOffset = 0 * cdef int readOffset = 0 # <<<<<<<<<<<<<< * cdef int cigarIndex = 0 * cdef int cigarLength = read.getCigarLength() */ __pyx_v_readOffset = 0; /* "variant.pyx":812 * cdef int refOffset = 0 * cdef int readOffset = 0 * cdef int cigarIndex = 0 # <<<<<<<<<<<<<< * cdef int cigarLength = read.getCigarLength() * cdef int index = 0 */ __pyx_v_cigarIndex = 0; /* "variant.pyx":813 * cdef int readOffset = 0 * cdef int cigarIndex = 0 * cdef int cigarLength = read.getCigarLength() # <<<<<<<<<<<<<< * cdef int index = 0 * cdef int baseQual = 0 */ __pyx_v_cigarLength = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->getCigarLength(__pyx_v_read); /* "variant.pyx":814 * cdef int cigarIndex = 0 * cdef int cigarLength = read.getCigarLength() * cdef int index = 0 # <<<<<<<<<<<<<< * cdef int baseQual = 0 * cdef int readIndex = 0 */ __pyx_v_index = 0; /* "variant.pyx":815 * cdef int cigarLength = read.getCigarLength() * cdef int index = 0 * cdef int baseQual = 0 # <<<<<<<<<<<<<< * cdef int readIndex = 0 * cdef int refIndex = 0 */ __pyx_v_baseQual = 0; /* "variant.pyx":816 * cdef int index = 0 * cdef int baseQual = 0 * cdef int readIndex = 0 # <<<<<<<<<<<<<< * cdef int refIndex = 0 * cdef int readLength = read.rlen() */ __pyx_v_readIndex = 0; /* "variant.pyx":817 * cdef int baseQual = 0 * cdef int readIndex = 0 * cdef int refIndex = 0 # <<<<<<<<<<<<<< * cdef int readLength = read.rlen() * cdef int isReverse = read.is_reverse() */ __pyx_v_refIndex = 0; /* "variant.pyx":818 * cdef int readIndex = 0 * cdef int refIndex = 0 * cdef int readLength = read.rlen() # <<<<<<<<<<<<<< * cdef int isReverse = read.is_reverse() * cdef char* readQual = read.qual() */ __pyx_v_readLength = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->rlen(__pyx_v_read); /* "variant.pyx":819 * cdef int refIndex = 0 * cdef int readLength = read.rlen() * cdef int isReverse = read.is_reverse() # <<<<<<<<<<<<<< * cdef char* readQual = read.qual() * cdef char* readSeq = read.seq() */ __pyx_v_isReverse = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->is_reverse(__pyx_v_read); /* "variant.pyx":820 * cdef int readLength = read.rlen() * cdef int isReverse = read.is_reverse() * cdef char* readQual = read.qual() # <<<<<<<<<<<<<< * cdef char* readSeq = read.seq() * cdef char readChar */ __pyx_v_readQual = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->qual(__pyx_v_read); /* "variant.pyx":821 * cdef int isReverse = read.is_reverse() * cdef char* readQual = read.qual() * cdef char* readSeq = read.seq() # <<<<<<<<<<<<<< * cdef char readChar * cdef char refChar */ __pyx_v_readSeq = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->seq(__pyx_v_read); /* "variant.pyx":824 * cdef char readChar * cdef char refChar * cdef list indelPos = [] # <<<<<<<<<<<<<< * * for cigarIndex from 0 <= cigarIndex < cigarLength: */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_indelPos = __pyx_t_1; __pyx_t_1 = 0; /* "variant.pyx":826 * cdef list indelPos = [] * * for cigarIndex from 0 <= cigarIndex < cigarLength: # <<<<<<<<<<<<<< * * flag = read.getCigarOpCode(cigarIndex) */ __pyx_t_2 = __pyx_v_cigarLength; for (__pyx_v_cigarIndex = 0; __pyx_v_cigarIndex < __pyx_t_2; __pyx_v_cigarIndex++) { /* "variant.pyx":828 * for cigarIndex from 0 <= cigarIndex < cigarLength: * * flag = read.getCigarOpCode(cigarIndex) # <<<<<<<<<<<<<< * length = read.getCigarOpLength(cigarIndex) * */ __pyx_v_flag = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->getCigarOpCode(__pyx_v_read, __pyx_v_cigarIndex); /* "variant.pyx":829 * * flag = read.getCigarOpCode(cigarIndex) * length = read.getCigarOpLength(cigarIndex) # <<<<<<<<<<<<<< * * # An insertion take us further along the read, but not the reference */ __pyx_v_length = ((struct __pyx_vtabstruct_15samtoolsWrapper_AlignedRead *)__pyx_v_read->__pyx_vtab)->getCigarOpLength(__pyx_v_read, __pyx_v_cigarIndex); /* "variant.pyx":832 * * # An insertion take us further along the read, but not the reference * if flag == self.CIGAR_I: # <<<<<<<<<<<<<< * * if isReverse: */ __pyx_t_3 = (__pyx_v_flag == __pyx_v_self->CIGAR_I); 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} else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_bamMaxPos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_9bamMaxPos_1__get__(o); } static int __pyx_setprop_7variant_7Variant_bamMaxPos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_7variant_7Variant_9bamMaxPos_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_minRefPos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_9minRefPos_1__get__(o); } static int __pyx_setprop_7variant_7Variant_minRefPos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_7variant_7Variant_9minRefPos_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_maxRefPos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_9maxRefPos_1__get__(o); 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} else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_hashValue(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_9hashValue_1__get__(o); } static int __pyx_setprop_7variant_7Variant_hashValue(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_7variant_7Variant_9hashValue_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_nAdded(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_6nAdded_1__get__(o); } static int __pyx_setprop_7variant_7Variant_nAdded(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_7variant_7Variant_6nAdded_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_nRemoved(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_8nRemoved_1__get__(o); } static int __pyx_setprop_7variant_7Variant_nRemoved(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_7variant_7Variant_8nRemoved_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_7variant_7Variant_varType(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_7variant_7Variant_7varType_1__get__(o); } static int __pyx_setprop_7variant_7Variant_varType(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_7variant_7Variant_7varType_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyMethodDef __pyx_methods_7variant_Variant[] = { {__Pyx_NAMESTR("shortRepr"), (PyCFunction)__pyx_pw_7variant_7Variant_11shortRepr, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_7variant_7Variant_10shortRepr)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_7variant_Variant[] = { {(char *)"refName", __pyx_getprop_7variant_7Variant_refName, __pyx_setprop_7variant_7Variant_refName, 0, 0}, {(char *)"added", __pyx_getprop_7variant_7Variant_added, __pyx_setprop_7variant_7Variant_added, 0, 0}, {(char *)"removed", __pyx_getprop_7variant_7Variant_removed, __pyx_setprop_7variant_7Variant_removed, 0, 0}, {(char *)"bamAdded", __pyx_getprop_7variant_7Variant_bamAdded, __pyx_setprop_7variant_7Variant_bamAdded, 0, 0}, {(char *)"bamRemoved", __pyx_getprop_7variant_7Variant_bamRemoved, __pyx_setprop_7variant_7Variant_bamRemoved, 0, 0}, {(char *)"refPos", __pyx_getprop_7variant_7Variant_refPos, __pyx_setprop_7variant_7Variant_refPos, 0, 0}, {(char *)"bamMinPos", __pyx_getprop_7variant_7Variant_bamMinPos, __pyx_setprop_7variant_7Variant_bamMinPos, 0, 0}, {(char *)"bamMaxPos", __pyx_getprop_7variant_7Variant_bamMaxPos, __pyx_setprop_7variant_7Variant_bamMaxPos, 0, 0}, {(char *)"minRefPos", __pyx_getprop_7variant_7Variant_minRefPos, __pyx_setprop_7variant_7Variant_minRefPos, 0, 0}, {(char *)"maxRefPos", __pyx_getprop_7variant_7Variant_maxRefPos, __pyx_setprop_7variant_7Variant_maxRefPos, 0, 0}, {(char *)"nSupportingReads", __pyx_getprop_7variant_7Variant_nSupportingReads, __pyx_setprop_7variant_7Variant_nSupportingReads, 0, 0}, {(char *)"varSource", __pyx_getprop_7variant_7Variant_varSource, __pyx_setprop_7variant_7Variant_varSource, 0, 0}, {(char *)"hashValue", __pyx_getprop_7variant_7Variant_hashValue, __pyx_setprop_7variant_7Variant_hashValue, 0, 0}, {(char *)"nAdded", __pyx_getprop_7variant_7Variant_nAdded, __pyx_setprop_7variant_7Variant_nAdded, 0, 0}, {(char *)"nRemoved", __pyx_getprop_7variant_7Variant_nRemoved, __pyx_setprop_7variant_7Variant_nRemoved, 0, 0}, {(char *)"varType", __pyx_getprop_7variant_7Variant_varType, __pyx_setprop_7variant_7Variant_varType, 0, 0}, {0, 0, 0, 0, 0} }; 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static PySequenceMethods __pyx_tp_as_sequence_Variant = { 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_Variant = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Variant = { #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_7variant_Variant = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("variant.Variant"), /*tp_name*/ sizeof(struct __pyx_obj_7variant_Variant), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_7variant_Variant, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif __pyx_pw_7variant_7Variant_9__repr__, /*tp_repr*/ &__pyx_tp_as_number_Variant, /*tp_as_number*/ &__pyx_tp_as_sequence_Variant, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Variant, /*tp_as_mapping*/ __pyx_pw_7variant_7Variant_3__hash__, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_7variant_7Variant_7__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Variant, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("\n Class to encapsulate information for all common variant types. The basic\n idea is to tread all variants as replacements, i.e. a certain sequence of\n bases is removed from the reference, and a certain sequence is added. A SNP is\n a replacement of 1 base with 1 different base, a deletion is a replacement of one\n sequence with a smaller sequence (or none at all), and an insertion is a replacement\n of one sequence with a longer sequence.\n "), /*tp_doc*/ __pyx_tp_traverse_7variant_Variant, /*tp_traverse*/ __pyx_tp_clear_7variant_Variant, /*tp_clear*/ __pyx_pw_7variant_7Variant_5__richcmp__, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_7variant_Variant, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_7variant_Variant, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_7variant_7Variant_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_7variant_Variant, /*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_7variant_VariantCandidateGenerator __pyx_vtable_7variant_VariantCandidateGenerator; static PyObject *__pyx_tp_new_7variant_VariantCandidateGenerator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_7variant_VariantCandidateGenerator *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_7variant_VariantCandidateGenerator *)o); p->__pyx_vtab = __pyx_vtabptr_7variant_VariantCandidateGenerator; p->variantHeap = ((PyObject*)Py_None); Py_INCREF(Py_None); p->pyRefSeq = ((PyObject*)Py_None); Py_INCREF(Py_None); p->rname = ((PyObject*)Py_None); Py_INCREF(Py_None); p->refFile = ((struct __pyx_obj_9fastafile_FastaFile *)Py_None); Py_INCREF(Py_None); p->options = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_7variant_VariantCandidateGenerator(PyObject *o) { struct __pyx_obj_7variant_VariantCandidateGenerator *p = (struct __pyx_obj_7variant_VariantCandidateGenerator *)o; Py_CLEAR(p->variantHeap); Py_CLEAR(p->pyRefSeq); Py_CLEAR(p->rname); Py_CLEAR(p->refFile); Py_CLEAR(p->options); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_7variant_VariantCandidateGenerator(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_7variant_VariantCandidateGenerator *p = (struct __pyx_obj_7variant_VariantCandidateGenerator *)o; if (p->variantHeap) { e = (*v)(p->variantHeap, a); if (e) return e; } if (p->pyRefSeq) { e = (*v)(p->pyRefSeq, a); if (e) return e; } if (p->rname) { e = (*v)(p->rname, a); if (e) return e; } if (p->refFile) { e = (*v)(((PyObject*)p->refFile), a); if (e) return e; } if (p->options) { e = (*v)(p->options, a); if (e) return e; } return 0; } static int __pyx_tp_clear_7variant_VariantCandidateGenerator(PyObject *o) { struct __pyx_obj_7variant_VariantCandidateGenerator *p = (struct __pyx_obj_7variant_VariantCandidateGenerator *)o; PyObject* tmp; tmp = ((PyObject*)p->variantHeap); p->variantHeap = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->pyRefSeq); p->pyRefSeq = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->rname); p->rname = ((PyObject*)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->refFile); p->refFile = ((struct __pyx_obj_9fastafile_FastaFile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->options); p->options = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_7variant_VariantCandidateGenerator[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_VariantCandidateGenerator = { 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_VariantCandidateGenerator = { 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_VariantCandidateGenerator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_VariantCandidateGenerator = { #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_7variant_VariantCandidateGenerator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("variant.VariantCandidateGenerator"), /*tp_name*/ sizeof(struct __pyx_obj_7variant_VariantCandidateGenerator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_7variant_VariantCandidateGenerator, /*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_VariantCandidateGenerator, /*tp_as_number*/ &__pyx_tp_as_sequence_VariantCandidateGenerator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_VariantCandidateGenerator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_VariantCandidateGenerator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("\n A class to generate variant candidates from a bunch of reads.\n "), /*tp_doc*/ __pyx_tp_traverse_7variant_VariantCandidateGenerator, /*tp_traverse*/ __pyx_tp_clear_7variant_VariantCandidateGenerator, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_7variant_VariantCandidateGenerator, /*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*/ 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__pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_23 = PyInt_FromLong(23); if (unlikely(!__pyx_int_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_24 = PyInt_FromLong(24); if (unlikely(!__pyx_int_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_100 = PyInt_FromLong(100); if (unlikely(!__pyx_int_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_2000 = PyInt_FromLong(2000); if (unlikely(!__pyx_int_2000)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; return 0; __pyx_L1_error:; return -1; } #if PY_MAJOR_VERSION < 3 PyMODINIT_FUNC initvariant(void); /*proto*/ PyMODINIT_FUNC initvariant(void) #else PyMODINIT_FUNC PyInit_variant(void); /*proto*/ PyMODINIT_FUNC PyInit_variant(void) #endif { PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; 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if (unlikely(!__pyx_vtabptr_15samtoolsWrapper_Samfile)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_15samtoolsWrapper_IteratorRow = __Pyx_ImportType("samtoolsWrapper", "IteratorRow", sizeof(struct __pyx_obj_15samtoolsWrapper_IteratorRow), 1); if (unlikely(!__pyx_ptype_15samtoolsWrapper_IteratorRow)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_vtabptr_15samtoolsWrapper_IteratorRow = (struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRow*)__Pyx_GetVtable(__pyx_ptype_15samtoolsWrapper_IteratorRow->tp_dict); if (unlikely(!__pyx_vtabptr_15samtoolsWrapper_IteratorRow)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_15samtoolsWrapper_IteratorRowAll = __Pyx_ImportType("samtoolsWrapper", "IteratorRowAll", sizeof(struct __pyx_obj_15samtoolsWrapper_IteratorRowAll), 1); if (unlikely(!__pyx_ptype_15samtoolsWrapper_IteratorRowAll)) {__pyx_filename = __pyx_f[3]; 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__Pyx_DECREF(((PyObject *)__pyx_v_7variant_indel_prior_model)); __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); __pyx_v_7variant_indel_prior_model = __pyx_t_3; __pyx_t_3 = 0; /* "variant.pyx":96 * * # Currently hard-coded insertion/deletion priors * cdef double complex_deletion_prior = 5e-5 # <<<<<<<<<<<<<< * cdef double complex_insertion_prior = 5e-6 * */ __pyx_v_7variant_complex_deletion_prior = 5e-5; /* "variant.pyx":97 * # Currently hard-coded insertion/deletion priors * cdef double complex_deletion_prior = 5e-5 * cdef double complex_insertion_prior = 5e-6 # <<<<<<<<<<<<<< * * ################################################################################################### */ __pyx_v_7variant_complex_insertion_prior = 5e-6; /* "variant.pyx":1 * """ # <<<<<<<<<<<<<< * Utility module, containing classes to handle reading and writing * files of variants. */ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; /* "samtoolsWrapper.pxd":385 * theRead.bitFlag |= BAM_FCOMPRESSED * * cdef inline void Read_SetUnCompressed(cAlignedRead* theRead): # <<<<<<<<<<<<<< * theRead.bitFlag &= (~BAM_FCOMPRESSED) * */ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); if (__pyx_m) { __Pyx_AddTraceback("init variant", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_ImportError, "init variant"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); #if PY_MAJOR_VERSION < 3 return; #else return __pyx_m; #endif } /* Runtime support code */ #if CYTHON_REFNANNY static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { PyObject *m = NULL, *p = NULL; 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"" : "s"); } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else 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; } #endif } static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; 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); #else PyErr_SetExcInfo(type, value, tb); #endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { /* try package relative import first */ PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: Py_XDECREF(empty_list); Py_XDECREF(py_import); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); #if PY_MAJOR_VERSION < 3 ctx = PyString_FromString(name); #else ctx = PyUnicode_FromString(name); #endif __Pyx_ErrRestore(old_exc, old_val, old_tb); if (!ctx) { PyErr_WriteUnraisable(Py_None); } else { PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } } 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_ExportVoidPtr(const char *name, void *p, const char *sig) { PyObject *d = 0; PyObject *cobj = 0; d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__"); if (!d) { PyErr_Clear(); d = PyDict_New(); if (!d) goto bad; Py_INCREF(d); if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0) goto bad; } #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3 && PY_MINOR_VERSION==0) cobj = PyCapsule_New(p, sig, 0); #else cobj = PyCObject_FromVoidPtrAndDesc(p, (void *)sig, 0); #endif if (!cobj) goto bad; if (PyDict_SetItemString(d, name, cobj) < 0) goto bad; Py_DECREF(cobj); Py_DECREF(d); return 0; bad: Py_XDECREF(cobj); Py_XDECREF(d); return -1; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, 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 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; } #ifndef __PYX_HAVE_RT_ImportFunction #define __PYX_HAVE_RT_ImportFunction static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { PyObject *d = 0; PyObject *cobj = 0; union { void (*fp)(void); void *p; } tmp; d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); if (!d) goto bad; cobj = PyDict_GetItemString(d, funcname); if (!cobj) { PyErr_Format(PyExc_ImportError, "%s does not export expected C function %s", PyModule_GetName(module), funcname); goto bad; } #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3 && PY_MINOR_VERSION==0) if (!PyCapsule_IsValid(cobj, sig)) { PyErr_Format(PyExc_TypeError, "C function %s.%s has wrong signature (expected %s, got %s)", PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); goto bad; } tmp.p = PyCapsule_GetPointer(cobj, sig); #else {const char *desc, *s1, *s2; desc = (const char *)PyCObject_GetDesc(cobj); if (!desc) goto bad; s1 = desc; s2 = sig; while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } if (*s1 != *s2) { PyErr_Format(PyExc_TypeError, "C function %s.%s has wrong signature (expected %s, got %s)", PyModule_GetName(module), funcname, sig, desc); goto bad; } tmp.p = PyCObject_AsVoidPtr(cobj);} #endif *f = tmp.fp; if (!(*f)) goto bad; Py_DECREF(d); return 0; bad: Py_XDECREF(d); return -1; } #endif 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 */