/* Generated by Cython 0.17.2 on Mon Sep 30 14:29:55 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)) ? 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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_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(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__cpopulation #define __PYX_HAVE_API__cpopulation #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[] = { "cpopulation.pyx", "fastafile.pxd", "samtoolsWrapper.pxd", "variant.pxd", "cwindow.pxd", "bamfileutils.pxd", "chaplotype.pxd", "cgenotype.pxd", }; /* "cpopulation.pyx":34 * ################################################################################################### * * ctypedef long long size_t # <<<<<<<<<<<<<< * * ################################################################################################### */ typedef PY_LONG_LONG __pyx_t_11cpopulation_size_t; /*--- Type declarations ---*/ struct __pyx_obj_7variant_VariantCandidateGenerator; struct __pyx_obj_10chaplotype_Haplotype; struct __pyx_obj_9fastafile_FastaFile; struct __pyx_obj_15samtoolsWrapper_AlignedRead; struct __pyx_obj_7cwindow_ReadArray; struct __pyx_obj_15samtoolsWrapper_IteratorRow; struct __pyx_obj_9cgenotype_HaploidGenotype; struct __pyx_obj_11cpopulation_Population; struct __pyx_obj_15samtoolsWrapper_Samfile; struct __pyx_obj_15samtoolsWrapper_IteratorRowAll; struct __pyx_obj_9cgenotype_DiploidGenotype; struct __pyx_obj_9fastafile_FastaIndex; struct __pyx_obj_12bamfileutils_MultiBamFileReader; struct __pyx_obj_12bamfileutils_MultiBamFileIterator; struct __pyx_obj_7cwindow_bamReadBuffer; 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; }; struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence; /* "chaplotype.pxd":47 * double* alignReads(self, int individualIndex, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenReadsStart, cAlignedRead** brokenReadsEnd, int useMapQualCap, int printAlignments) * double alignSingleRead(self, cAlignedRead* theRead, int useMapQualCap, int printAlignments) * char* getReferenceSequence(self, prefix=*) # <<<<<<<<<<<<<< * char* getMutatedSequence(self) * dict vcfINFO(self) */ struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence { int __pyx_n; PyObject *prefix; }; struct __pyx_opt_args_11cpopulation_10Population_calculatePosterior; /* "cpopulation.pxd":49 * # Class functions * cdef: * double calculatePosterior(self, Variant var, int flatPrior=*) # <<<<<<<<<<<<<< * void computeVariantPosteriors(self) * void computeVariantINFO(self) */ struct __pyx_opt_args_11cpopulation_10Population_calculatePosterior { int __pyx_n; int flatPrior; }; /* "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; }; /* "chaplotype.pxd":14 * cdef int computeOverlapOfReadAndHaplotype(int hapStart, int hapEnd, cAlignedRead* theRead) * * cdef class Haplotype: # <<<<<<<<<<<<<< * cdef: * bytes refName */ struct __pyx_obj_10chaplotype_Haplotype { PyObject_HEAD struct __pyx_vtabstruct_10chaplotype_Haplotype *__pyx_vtab; PyObject *refName; int startPos; int endPos; int maxReadLength; int minVarPos; int maxVarPos; PyObject *variants; PyObject *haplotypeSequence; char *cHaplotypeSequence; struct __pyx_obj_9fastafile_FastaFile *refFile; PyObject *options; double *likelihoodCache; int lenCache; int lastIndividualIndex; PyObject *referenceSequence; int hash; int hapLen; int hasIndel; int nBaseChangesFromRef; int verbosity; int endBufferSize; char *cHomopolQ; short *localGapOpen; short *hapSequenceHash; short *hapSequenceNextArray; PyObject *indelErrorModel; int useIndelErrorModel; PyObject *localGapOpenQ; char *cLocalGapOpenQ; }; /* "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; }; /* "cwindow.pxd":14 * ################################################################################################### * * cdef class ReadArray: # <<<<<<<<<<<<<< * cdef cAlignedRead** array * cdef cAlignedRead** windowStart */ struct __pyx_obj_7cwindow_ReadArray { PyObject_HEAD struct __pyx_vtabstruct_7cwindow_ReadArray *__pyx_vtab; __pyx_t_15samtoolsWrapper_cAlignedRead **array; __pyx_t_15samtoolsWrapper_cAlignedRead **windowStart; __pyx_t_15samtoolsWrapper_cAlignedRead **windowEnd; int __pyx___size; int __pyx___capacity; int __pyx___longestRead; }; /* "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; }; /* "cgenotype.pxd":15 * cdef double calculateDataLikelihood(DiploidGenotype self, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadsStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenMatesStart, cAlignedRead** brokenMatesEnd, int individualIndex, int nIndividuals, double* gof, int printAlignments) * * cdef class HaploidGenotype: # <<<<<<<<<<<<<< * cdef Haplotype hap1 * cdef double calculateDataLikelihood(self, cAlignedRead** start, cAlignedRead** end, int individualIndex, int nIndividuals) */ struct __pyx_obj_9cgenotype_HaploidGenotype { PyObject_HEAD struct __pyx_vtabstruct_9cgenotype_HaploidGenotype *__pyx_vtab; struct __pyx_obj_10chaplotype_Haplotype *hap1; }; /* "cpopulation.pxd":12 * ################################################################################################### * * cdef class Population: # <<<<<<<<<<<<<< * * # Class variables */ struct __pyx_obj_11cpopulation_Population { PyObject_HEAD struct __pyx_vtabstruct_11cpopulation_Population *__pyx_vtab; PyObject *vcfInfo; PyObject *vcfFilter; PyObject *varsByPos; PyObject *variantPosteriors; PyObject *genotypeCalls; PyObject *variants; PyObject *haplotypes; PyObject *genotypes; double **genotypeLikelihoods; double **goodnessOfFitValues; double **EMLikelihoods; double *frequencies; double *newFrequencies; int **haplotypeIndexes; int *nReads; double *maxLogLikelihoods; double *freqsPrimeByHapIndex; int nVariants; int nHaplotypes; int nIndividuals; int maxHaplotypes; int maxGenotypes; int ploidy; int nGenotypes; int verbosity; int printAlignments; int useEMLikelihoods; PyObject *readBuffers; struct __pyx_obj_9fastafile_FastaFile *refFile; PyObject *options; }; /* "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; }; /* "cgenotype.pxd":8 * from samtoolsWrapper cimport cAlignedRead * * cdef class DiploidGenotype: # <<<<<<<<<<<<<< * cdef Haplotype hap1 * cdef Haplotype hap2 */ struct __pyx_obj_9cgenotype_DiploidGenotype { PyObject_HEAD struct __pyx_vtabstruct_9cgenotype_DiploidGenotype *__pyx_vtab; struct __pyx_obj_10chaplotype_Haplotype *hap1; struct __pyx_obj_10chaplotype_Haplotype *hap2; double hap1Like; double hap2Like; }; /* "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; }; /* "cwindow.pxd":29 * ################################################################################################### * * cdef class bamReadBuffer: # <<<<<<<<<<<<<< * cdef char* chrom * cdef int chromID */ struct __pyx_obj_7cwindow_bamReadBuffer { PyObject_HEAD struct __pyx_vtabstruct_7cwindow_bamReadBuffer *__pyx_vtab; char *chrom; int chromID; int *filteredReadCountsByType; int isSorted; int startBase; int endBase; int windowStartBase; int windowEndBase; int maxReads; int minMapQual; int verbosity; int minGoodBases; __pyx_t_15samtoolsWrapper_cAlignedRead *lastRead; PyObject *sample; struct __pyx_obj_7cwindow_ReadArray *reads; struct __pyx_obj_7cwindow_ReadArray *badReads; struct __pyx_obj_7cwindow_ReadArray *brokenMates; }; /* "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; }; /* "cwindow.pxd":14 * ################################################################################################### * * cdef class ReadArray: # <<<<<<<<<<<<<< * cdef cAlignedRead** array * cdef cAlignedRead** windowStart */ struct __pyx_vtabstruct_7cwindow_ReadArray { int (*getSize)(struct __pyx_obj_7cwindow_ReadArray *); void (*append)(struct __pyx_obj_7cwindow_ReadArray *, __pyx_t_15samtoolsWrapper_cAlignedRead *); void (*setWindowPointers)(struct __pyx_obj_7cwindow_ReadArray *, int, int); void (*setWindowPointersBasedOnMatePos)(struct __pyx_obj_7cwindow_ReadArray *, int, int); int (*getLengthOfLongestRead)(struct __pyx_obj_7cwindow_ReadArray *); }; static struct __pyx_vtabstruct_7cwindow_ReadArray *__pyx_vtabptr_7cwindow_ReadArray; /* "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; /* "cwindow.pxd":29 * ################################################################################################### * * cdef class bamReadBuffer: # <<<<<<<<<<<<<< * cdef char* chrom * cdef int chromID */ struct __pyx_vtabstruct_7cwindow_bamReadBuffer { void (*setWindowPointers)(struct __pyx_obj_7cwindow_bamReadBuffer *, int, int, int, int, char *, int); void (*recompressReadsInCurrentWindow)(struct __pyx_obj_7cwindow_bamReadBuffer *, int, int, char *, int, int); void (*addReadToBuffer)(struct __pyx_obj_7cwindow_bamReadBuffer *, __pyx_t_15samtoolsWrapper_cAlignedRead *); int (*countImproperPairs)(struct __pyx_obj_7cwindow_bamReadBuffer *); int (*countAlignmentGaps)(struct __pyx_obj_7cwindow_bamReadBuffer *); void (*sortReads)(struct __pyx_obj_7cwindow_bamReadBuffer *); void (*sortBrokenMates)(struct __pyx_obj_7cwindow_bamReadBuffer *); void (*logFilterSummary)(struct __pyx_obj_7cwindow_bamReadBuffer *); }; static struct __pyx_vtabstruct_7cwindow_bamReadBuffer *__pyx_vtabptr_7cwindow_bamReadBuffer; /* "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; /* "chaplotype.pxd":14 * cdef int computeOverlapOfReadAndHaplotype(int hapStart, int hapEnd, cAlignedRead* theRead) * * cdef class Haplotype: # <<<<<<<<<<<<<< * cdef: * bytes refName */ struct __pyx_vtabstruct_10chaplotype_Haplotype { double *(*alignReads)(struct __pyx_obj_10chaplotype_Haplotype *, int, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, int, int); double (*alignSingleRead)(struct __pyx_obj_10chaplotype_Haplotype *, __pyx_t_15samtoolsWrapper_cAlignedRead *, int, int); char *(*getReferenceSequence)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_opt_args_10chaplotype_9Haplotype_getReferenceSequence *__pyx_optional_args); char *(*getMutatedSequence)(struct __pyx_obj_10chaplotype_Haplotype *); PyObject *(*vcfINFO)(struct __pyx_obj_10chaplotype_Haplotype *); PyObject *(*getSequenceContext)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *); int (*homopolymerLengthForOneVariant)(struct __pyx_obj_10chaplotype_Haplotype *, struct __pyx_obj_7variant_Variant *); PyObject *(*homopolymerLengths)(struct __pyx_obj_10chaplotype_Haplotype *); void (*annotateWithGapOpen)(struct __pyx_obj_10chaplotype_Haplotype *); }; static struct __pyx_vtabstruct_10chaplotype_Haplotype *__pyx_vtabptr_10chaplotype_Haplotype; /* "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.pxd":42 * ################################################################################################### * * cdef class VariantCandidateGenerator: # <<<<<<<<<<<<<< * cdef int CIGAR_M * cdef int CIGAR_I */ 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; /* "cgenotype.pxd":8 * from samtoolsWrapper cimport cAlignedRead * * cdef class DiploidGenotype: # <<<<<<<<<<<<<< * cdef Haplotype hap1 * cdef Haplotype hap2 */ struct __pyx_vtabstruct_9cgenotype_DiploidGenotype { double (*calculateDataLikelihood)(struct __pyx_obj_9cgenotype_DiploidGenotype *, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, int, int, double *, int); }; static struct __pyx_vtabstruct_9cgenotype_DiploidGenotype *__pyx_vtabptr_9cgenotype_DiploidGenotype; /* "cpopulation.pyx":85 * ################################################################################################### * * cdef class Population: # <<<<<<<<<<<<<< * """ * The Population Caller takes a list of haplotypes and a list of reads and */ struct __pyx_vtabstruct_11cpopulation_Population { double (*calculatePosterior)(struct __pyx_obj_11cpopulation_Population *, struct __pyx_obj_7variant_Variant *, struct __pyx_opt_args_11cpopulation_10Population_calculatePosterior *__pyx_optional_args); void (*computeVariantPosteriors)(struct __pyx_obj_11cpopulation_Population *); void (*computeVariantINFO)(struct __pyx_obj_11cpopulation_Population *); void (*reset)(struct __pyx_obj_11cpopulation_Population *); void (*computeVariantFILTER)(struct __pyx_obj_11cpopulation_Population *); void (*callGenotypes)(struct __pyx_obj_11cpopulation_Population *); void (*call)(struct __pyx_obj_11cpopulation_Population *, int, int); double (*EMiteration)(struct __pyx_obj_11cpopulation_Population *, double *, double *); void (*setup)(struct __pyx_obj_11cpopulation_Population *, PyObject *, PyObject *, PyObject *, int, int, int, PyObject *); }; static struct __pyx_vtabstruct_11cpopulation_Population *__pyx_vtabptr_11cpopulation_Population; /* "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; /* "variant.pxd":16 * ################################################################################################### * * cdef class Variant: # <<<<<<<<<<<<<< * cdef: * public bytes refName */ 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":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 *); 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}; 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 *); }; static struct __pyx_vtabstruct_15samtoolsWrapper_IteratorRow *__pyx_vtabptr_15samtoolsWrapper_IteratorRow; /* "cgenotype.pxd":15 * cdef double calculateDataLikelihood(DiploidGenotype self, cAlignedRead** start, cAlignedRead** end, cAlignedRead** badReadsStart, cAlignedRead** badReadsEnd, cAlignedRead** brokenMatesStart, cAlignedRead** brokenMatesEnd, int individualIndex, int nIndividuals, double* gof, int printAlignments) * * cdef class HaploidGenotype: # <<<<<<<<<<<<<< * cdef Haplotype hap1 * cdef double calculateDataLikelihood(self, cAlignedRead** start, cAlignedRead** end, int individualIndex, int nIndividuals) */ struct __pyx_vtabstruct_9cgenotype_HaploidGenotype { double (*calculateDataLikelihood)(struct __pyx_obj_9cgenotype_HaploidGenotype *, __pyx_t_15samtoolsWrapper_cAlignedRead **, __pyx_t_15samtoolsWrapper_cAlignedRead **, int, int); 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r = PyObject_CallFunctionObjArgs(m, x, NULL); Py_DECREF(m); return r; } } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { int result = PySequence_Contains(seq, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } #if PY_VERSION_HEX < 0x02050000 #ifndef PyAnySet_CheckExact #define PyAnySet_CheckExact(ob) \ ((ob)->ob_type == &PySet_Type || \ (ob)->ob_type == &PyFrozenSet_Type) #define PySet_New(iterable) \ PyObject_CallFunctionObjArgs((PyObject *)&PySet_Type, (iterable), NULL) #define Pyx_PyFrozenSet_New(iterable) \ PyObject_CallFunctionObjArgs((PyObject *)&PyFrozenSet_Type, (iterable), NULL) #define PySet_Size(anyset) \ PyObject_Size((anyset)) #define PySet_Contains(anyset, key) \ PySequence_Contains((anyset), (key)) #define PySet_Pop(set) \ PyObject_CallMethod(set, (char *)"pop", NULL) static CYTHON_INLINE int PySet_Clear(PyObject *set) { PyObject *ret = PyObject_CallMethod(set, (char *)"clear", NULL); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char *)"discard", (char *)"O", key); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char *)"add", (char *)"O", key); if (!ret) return -1; Py_DECREF(ret); return 0; } #endif /* PyAnySet_CheckExact (<= Py2.4) */ #endif /* < Py2.5 */ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ #define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_SetItemInt_Fast(o, i, v) : \ __Pyx_SetItemInt_Generic(o, to_py_func(i), v)) static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { int r; if (!j) return -1; r = PyObject_SetItem(o, j, v); Py_DECREF(j); return r; } static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) { #if CYTHON_COMPILING_IN_CPYTHON if (PyList_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { PyObject* old = PyList_GET_ITEM(o, n); Py_INCREF(v); PyList_SET_ITEM(o, n, v); Py_DECREF(old); return 1; } } else { /* inlined PySequence_SetItem() */ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_ass_item)) { if (unlikely(i < 0) && likely(m->sq_length)) { Py_ssize_t l = m->sq_length(o); if (unlikely(l < 0)) return -1; i += l; } return m->sq_ass_item(o, i, v); } } #else #if CYTHON_COMPILING_IN_PYPY if (PySequence_Check(o) && !PyDict_Check(o)) { #else if (PySequence_Check(o)) { #endif return PySequence_SetItem(o, i, v); } #endif return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename); /*proto*/ static int __Pyx_check_binary_version(void); static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ static int __Pyx_ImportVoidPtr(PyObject *module, const char *name, void **p, const char *sig); /*proto*/ static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'fastafile' */ static PyTypeObject *__pyx_ptype_9fastafile_FastaIndex = 0; static PyTypeObject *__pyx_ptype_9fastafile_FastaFile = 0; /* Module declarations from 'samtoolsWrapper' */ static PyTypeObject *__pyx_ptype_15samtoolsWrapper_Samfile = 0; static PyTypeObject *__pyx_ptype_15samtoolsWrapper_IteratorRow = 0; static PyTypeObject *__pyx_ptype_15samtoolsWrapper_IteratorRowAll = 0; static PyTypeObject *__pyx_ptype_15samtoolsWrapper_AlignedRead = 0; /* Module declarations from 'variant' */ static PyTypeObject *__pyx_ptype_7variant_Variant = 0; static PyTypeObject *__pyx_ptype_7variant_VariantCandidateGenerator = 0; static int *__pyx_vp_7variant_PLATYPUS_VAR = 0; #define __pyx_v_7variant_PLATYPUS_VAR (*__pyx_vp_7variant_PLATYPUS_VAR) static int *__pyx_vp_7variant_FILE_VAR = 0; #define __pyx_v_7variant_FILE_VAR (*__pyx_vp_7variant_FILE_VAR) static int *__pyx_vp_7variant_ASSEMBLER_VAR = 0; #define __pyx_v_7variant_ASSEMBLER_VAR (*__pyx_vp_7variant_ASSEMBLER_VAR) /* Module declarations from 'cython' */ /* Module declarations from 'cwindow' */ static PyTypeObject *__pyx_ptype_7cwindow_ReadArray = 0; static PyTypeObject *__pyx_ptype_7cwindow_bamReadBuffer = 0; /* 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 'chaplotype' */ static PyTypeObject *__pyx_ptype_10chaplotype_Haplotype = 0; /* Module declarations from 'cgenotype' */ static PyTypeObject *__pyx_ptype_9cgenotype_DiploidGenotype = 0; static PyTypeObject *__pyx_ptype_9cgenotype_HaploidGenotype = 0; /* Module declarations from 'vcfutils' */ static PyObject *(*__pyx_f_8vcfutils_vcfINFO)(double *, PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, int, PyObject *, struct __pyx_obj_9fastafile_FastaFile *); /*proto*/ static PyObject *(*__pyx_f_8vcfutils_vcfFILTER)(PyObject *, PyObject *, PyObject *, PyObject *, PyObject *); /*proto*/ /* Module declarations from 'cerrormodel' */ /* Module declarations from 'cpopulation' */ static PyTypeObject *__pyx_ptype_11cpopulation_Population = 0; static double __pyx_v_11cpopulation_PI; static double __pyx_v_11cpopulation_mLTOT; static void __pyx_f_11cpopulation_my_free(void *); /*proto*/ static void *__pyx_f_11cpopulation_my_calloc(size_t, size_t); /*proto*/ #define __Pyx_MODULE_NAME "cpopulation" int __pyx_module_is_main_cpopulation = 0; /* Implementation of 'cpopulation' */ static PyObject *__pyx_builtin_StandardError; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_sorted; static int __pyx_pf_11cpopulation_10Population___init__(struct __pyx_obj_11cpopulation_Population *__pyx_v_self, PyObject *__pyx_v_options); /* proto */ static void __pyx_pf_11cpopulation_10Population_2__dealloc__(struct __pyx_obj_11cpopulation_Population *__pyx_v_self); /* proto */ static char __pyx_k_1[] = "nInd != len(readBuffers). Something is very wrong here. Quitting now."; static char __pyx_k_3[] = "Variants = %s"; static char __pyx_k_4[] = "nVariants = %s. nHaplotypes = %s. nGenotypes = %s"; static char __pyx_k_5[] = "Error in cPopulation.setup"; static char __pyx_k_6[] = "nGenotypes > options.maxGenotypes. (%s > %s). Something is very wrong here. Quitting now."; static char __pyx_k_7[] = "nHaplotypes > options.maxHaplotypes. (%s > %s). Something is very wrong here. Quitting now."; static char __pyx_k_8[] = "Population constructed with %s haplotypes, %s genotypes and %s samples"; static char __pyx_k_9[] = "Printing all haplotypes in population and their sequences..."; static char __pyx_k_11[] = "%s\t%s"; static char __pyx_k_12[] = "Done printing all haplotypes in population..."; static char __pyx_k_14[] = ""; static char __pyx_k_16[] = "####################################################################"; static char __pyx_k_18[] = "Read alignment Likelihood debug information (top 10 genotypes)"; static char __pyx_k_22[] = "Sample\tPhred-likelihood\tNumber of reads\tGenotype"; static char __pyx_k_24[] = "%s\t%s\t%s\t%s"; static char __pyx_k_25[] = "Verbose output: logging likelihoods for each read..."; static char __pyx_k_28[] = "For Genotype %s"; static char __pyx_k_29[] = "Hap1 start = %s. end = %s. Hap1 start = %s. end = %s."; static char __pyx_k_30[] = "Logging haplotype sequences..."; static char __pyx_k_33[] = "Sample\tRead\tLL Hap1\tLL Hap2\tGL So Far\tRead MapQ\tRead Start\tRead End"; static char __pyx_k_35[] = "%s\t%s\t%1.2f\t%1.2f\t%1.2f\t%s\t%s\t%s"; static char __pyx_k_37[] = "#####################################################################################################"; static char __pyx_k_41[] = "#########################################################################"; static char __pyx_k_43[] = "Posterior calculation debug information"; static char __pyx_k_47[] = "Computing posterior for variants %s. N haplotypes = %s. n Ind = %s"; static char __pyx_k_48[] = "Sum of frequencies of haplotypes containing variant %s = %s"; static char __pyx_k_49[] = "Haplotype\tUn-scaled freq\tScaled freq"; static char __pyx_k_51[] = "%s\t%s\t%s"; static char __pyx_k_53[] = "Sample\tLikelihood\tfreqHap1\tfreqHap2\tscaledFreq1\tscaledFreq2\tsumVar\tsumNoVar\tGenotype"; static char __pyx_k_55[] = "%s\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%s"; static char __pyx_k_56[] = "For variant %s, post = %.20f. 1-post = %s. max(1e-20, 1-post) = %s"; static char __pyx_k_57[] = "For variant %s, Prior = %s. Ratio = %s. Post = %s. SumLogProbNoVar = %s. SumLogProbVar = %s"; static char __pyx_k_58[] = "Variant phred score = %s"; static char __pyx_k_61[] = "EM Likelihood debug information"; static char __pyx_k_65[] = "Sample\tEM Likelihood\tGenotype"; static char __pyx_k_67[] = "useEM = %s"; static char __pyx_k_68[] = "Called genotype %s for indiviual %s"; static char __pyx_k_71[] = "EM Iteration debug information"; static char __pyx_k_75[] = "Done %s EM iterations. Max change = %s"; static char __pyx_k_76[] = "Haplotype\tFrequency"; static char __pyx_k_78[] = "EM Stats: Final Max Frequency Change = %s. nIterations = %s"; static char __pyx_k_79[] = "\nThis module implements the core EM algorithm for inferring population\nhaplotype frequencies.\n"; static char __pyx_k__pi[] = "pi"; static char __pyx_k__Log[] = "Log"; static char __pyx_k__info[] = "info"; static char __pyx_k__math[] = "math"; static char __pyx_k__nInd[] = "nInd"; static char __pyx_k__debug[] = "debug"; static char __pyx_k__error[] = "error"; static char __pyx_k__logger[] = "logger"; static char __pyx_k__ploidy[] = "ploidy"; static char __pyx_k__random[] = "random"; static char __pyx_k__sorted[] = "sorted"; static char __pyx_k__cwindow[] = "cwindow"; static char __pyx_k__logging[] = "logging"; static char __pyx_k__options[] = "options"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__getLogger[] = "getLogger"; 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/* "cpopulation.pyx":290 * theBuffer = self.readBuffers[individualIndex] * nReadsThisInd = theBuffer.reads.windowEnd - theBuffer.reads.windowStart * self.nReads[individualIndex] = nReadsThisInd # <<<<<<<<<<<<<< * self.maxLogLikelihoods[individualIndex] = -1e7 * */ (__pyx_v_self->nReads[__pyx_v_individualIndex]) = __pyx_v_nReadsThisInd; /* "cpopulation.pyx":291 * nReadsThisInd = theBuffer.reads.windowEnd - theBuffer.reads.windowStart * self.nReads[individualIndex] = nReadsThisInd * self.maxLogLikelihoods[individualIndex] = -1e7 # <<<<<<<<<<<<<< * * for genotypeIndex from 0 <= genotypeIndex < self.nGenotypes: */ (__pyx_v_self->maxLogLikelihoods[__pyx_v_individualIndex]) = -1e7; /* "cpopulation.pyx":293 * self.maxLogLikelihoods[individualIndex] = -1e7 * * for genotypeIndex from 0 <= genotypeIndex < self.nGenotypes: # <<<<<<<<<<<<<< * genotype = genotypes[genotypeIndex] * */ __pyx_t_10 = __pyx_v_self->nGenotypes; for (__pyx_v_genotypeIndex = 0; __pyx_v_genotypeIndex < __pyx_t_10; __pyx_v_genotypeIndex++) { /* "cpopulation.pyx":294 * * for genotypeIndex from 0 <= genotypeIndex < self.nGenotypes: * genotype = genotypes[genotypeIndex] # <<<<<<<<<<<<<< * * if nReadsThisInd == 0: */ if (unlikely(((PyObject *)__pyx_v_genotypes) == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); 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/* "cpopulation.pyx":301 * logLikelihood = genotype.calculateDataLikelihood(theBuffer.reads.windowStart, theBuffer.reads.windowEnd, theBuffer.badReads.windowStart, theBuffer.badReads.windowEnd, theBuffer.brokenMates.windowStart, theBuffer.brokenMates.windowEnd, individualIndex, self.nIndividuals, self.goodnessOfFitValues[genotypeIndex], self.printAlignments) * * if logLikelihood > self.maxLogLikelihoods[individualIndex]: # <<<<<<<<<<<<<< * self.maxLogLikelihoods[individualIndex] = logLikelihood * */ __pyx_t_2 = (__pyx_v_logLikelihood > (__pyx_v_self->maxLogLikelihoods[__pyx_v_individualIndex])); if (__pyx_t_2) { /* "cpopulation.pyx":302 * * if logLikelihood > self.maxLogLikelihoods[individualIndex]: * self.maxLogLikelihoods[individualIndex] = logLikelihood # <<<<<<<<<<<<<< * * self.genotypeLikelihoods[individualIndex][genotypeIndex] = logLikelihood */ (__pyx_v_self->maxLogLikelihoods[__pyx_v_individualIndex]) = __pyx_v_logLikelihood; goto __pyx_L17; } __pyx_L17:; /* "cpopulation.pyx":304 * self.maxLogLikelihoods[individualIndex] = logLikelihood * * self.genotypeLikelihoods[individualIndex][genotypeIndex] = logLikelihood # <<<<<<<<<<<<<< * * # Re-scale all genotype likelihoods using the maximum value */ ((__pyx_v_self->genotypeLikelihoods[__pyx_v_individualIndex])[__pyx_v_genotypeIndex]) = __pyx_v_logLikelihood; 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/* "cpopulation.pyx":421 * * likelihoodThisGenotype = genotypeLikelihoodsThisIndividual[j] * s = self.haplotypeIndexes[j][0] # <<<<<<<<<<<<<< * r = self.haplotypeIndexes[j][1] * thisCSR = likelihoodThisGenotype*freq[s]*freq[r]*(1 + (r != s)) */ __pyx_v_s = ((__pyx_v_self->haplotypeIndexes[__pyx_v_j])[0]); /* "cpopulation.pyx":422 * likelihoodThisGenotype = genotypeLikelihoodsThisIndividual[j] * s = self.haplotypeIndexes[j][0] * r = self.haplotypeIndexes[j][1] # <<<<<<<<<<<<<< * thisCSR = likelihoodThisGenotype*freq[s]*freq[r]*(1 + (r != s)) * csr[j] = thisCSR */ __pyx_v_r = ((__pyx_v_self->haplotypeIndexes[__pyx_v_j])[1]); /* "cpopulation.pyx":423 * s = self.haplotypeIndexes[j][0] * r = self.haplotypeIndexes[j][1] * thisCSR = likelihoodThisGenotype*freq[s]*freq[r]*(1 + (r != s)) # <<<<<<<<<<<<<< * csr[j] = thisCSR * csrSum += thisCSR */ __pyx_v_thisCSR = (((__pyx_v_likelihoodThisGenotype * (__pyx_v_freq[__pyx_v_s])) * (__pyx_v_freq[__pyx_v_r])) * (1 + (__pyx_v_r != __pyx_v_s))); /* "cpopulation.pyx":424 * r = self.haplotypeIndexes[j][1] * thisCSR = likelihoodThisGenotype*freq[s]*freq[r]*(1 + (r != s)) * csr[j] = thisCSR # <<<<<<<<<<<<<< * csrSum += thisCSR * */ (__pyx_v_csr[__pyx_v_j]) = __pyx_v_thisCSR; /* "cpopulation.pyx":425 * thisCSR = likelihoodThisGenotype*freq[s]*freq[r]*(1 + (r != s)) * csr[j] = thisCSR * csrSum += thisCSR # <<<<<<<<<<<<<< * * # Normalisation */ __pyx_v_csrSum = (__pyx_v_csrSum + __pyx_v_thisCSR); } /* "cpopulation.pyx":428 * * # Normalisation * if csrSum > 0.0: # <<<<<<<<<<<<<< * for j from 0 <= j < self.nGenotypes: * csr[j] /= csrSum */ __pyx_t_2 = (__pyx_v_csrSum > 0.0); if (__pyx_t_2) { /* "cpopulation.pyx":429 * # Normalisation * if csrSum > 0.0: * for j from 0 <= j < self.nGenotypes: # <<<<<<<<<<<<<< * csr[j] /= csrSum * */ __pyx_t_3 = __pyx_v_self->nGenotypes; for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) { /* "cpopulation.pyx":430 * if csrSum > 0.0: * for j from 0 <= j < self.nGenotypes: * csr[j] /= csrSum # <<<<<<<<<<<<<< * * #for k from 0 <= k < self.nHaplotypes: */ __pyx_t_4 = __pyx_v_j; (__pyx_v_csr[__pyx_t_4]) = ((__pyx_v_csr[__pyx_t_4]) / __pyx_v_csrSum); } goto __pyx_L8; } __pyx_L8:; __pyx_L3_continue:; } /* "cpopulation.pyx":468 * # New, better implementation. Linear in nIndividuals and nGenotypes * # Set all temp frequencies to 0 * for k from 0 <= k < self.nHaplotypes: # <<<<<<<<<<<<<< * newFreqs[k] = 0.0 * */ __pyx_t_1 = __pyx_v_self->nHaplotypes; for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) { /* "cpopulation.pyx":469 * # Set all temp frequencies to 0 * for k from 0 <= k < self.nHaplotypes: * newFreqs[k] = 0.0 # <<<<<<<<<<<<<< * * for i from 0 <= i < self.nIndividuals: */ (__pyx_v_newFreqs[__pyx_v_k]) = 0.0; } /* "cpopulation.pyx":471 * newFreqs[k] = 0.0 * * for i from 0 <= i < self.nIndividuals: # <<<<<<<<<<<<<< * * if self.nReads[i] == 0: */ __pyx_t_1 = __pyx_v_self->nIndividuals; for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) { /* "cpopulation.pyx":473 * for i from 0 <= i < self.nIndividuals: * * if self.nReads[i] == 0: # <<<<<<<<<<<<<< * continue * */ __pyx_t_2 = ((__pyx_v_self->nReads[__pyx_v_i]) == 0); if (__pyx_t_2) { /* "cpopulation.pyx":474 * * if self.nReads[i] == 0: * continue # <<<<<<<<<<<<<< * * csr = self.EMLikelihoods[i] */ goto __pyx_L13_continue; goto __pyx_L15; } __pyx_L15:; /* "cpopulation.pyx":476 * continue * * csr = self.EMLikelihoods[i] # <<<<<<<<<<<<<< * * for j from 0 <= j < self.nGenotypes: */ __pyx_v_csr = (__pyx_v_self->EMLikelihoods[__pyx_v_i]); /* "cpopulation.pyx":478 * csr = self.EMLikelihoods[i] * * for j from 0 <= j < self.nGenotypes: # <<<<<<<<<<<<<< * thisCSR = csr[j] * s = self.haplotypeIndexes[j][0] */ __pyx_t_3 = __pyx_v_self->nGenotypes; for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) { /* "cpopulation.pyx":479 * * for j from 0 <= j < self.nGenotypes: * thisCSR = csr[j] # <<<<<<<<<<<<<< * s = self.haplotypeIndexes[j][0] * r = self.haplotypeIndexes[j][1] */ __pyx_v_thisCSR = (__pyx_v_csr[__pyx_v_j]); /* "cpopulation.pyx":480 * for j from 0 <= j < self.nGenotypes: * thisCSR = csr[j] * s = self.haplotypeIndexes[j][0] # <<<<<<<<<<<<<< * r = self.haplotypeIndexes[j][1] * newFreqs[s] += thisCSR */ __pyx_v_s = ((__pyx_v_self->haplotypeIndexes[__pyx_v_j])[0]); /* "cpopulation.pyx":481 * thisCSR = csr[j] * s = self.haplotypeIndexes[j][0] * r = self.haplotypeIndexes[j][1] # <<<<<<<<<<<<<< * newFreqs[s] += thisCSR * newFreqs[r] += thisCSR */ __pyx_v_r = ((__pyx_v_self->haplotypeIndexes[__pyx_v_j])[1]); /* "cpopulation.pyx":482 * s = self.haplotypeIndexes[j][0] * r = self.haplotypeIndexes[j][1] * newFreqs[s] += thisCSR # <<<<<<<<<<<<<< * newFreqs[r] += thisCSR * */ __pyx_t_4 = __pyx_v_s; (__pyx_v_newFreqs[__pyx_t_4]) = ((__pyx_v_newFreqs[__pyx_t_4]) + __pyx_v_thisCSR); /* "cpopulation.pyx":483 * r = self.haplotypeIndexes[j][1] * newFreqs[s] += thisCSR * newFreqs[r] += thisCSR # <<<<<<<<<<<<<< * * for k from 0 <= k < self.nHaplotypes: */ __pyx_t_4 = __pyx_v_r; (__pyx_v_newFreqs[__pyx_t_4]) = ((__pyx_v_newFreqs[__pyx_t_4]) + __pyx_v_thisCSR); } __pyx_L13_continue:; } /* "cpopulation.pyx":485 * newFreqs[r] += thisCSR * * for k from 0 <= k < self.nHaplotypes: # <<<<<<<<<<<<<< * newFreqs[k] = newFreqs[k]/(self.ploidy*nIndWithData) * freqChange = fabs(freq[k] - newFreqs[k]) */ __pyx_t_1 = __pyx_v_self->nHaplotypes; for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) { /* "cpopulation.pyx":486 * * for k from 0 <= k < self.nHaplotypes: * newFreqs[k] = newFreqs[k]/(self.ploidy*nIndWithData) # <<<<<<<<<<<<<< * freqChange = fabs(freq[k] - newFreqs[k]) * */ (__pyx_v_newFreqs[__pyx_v_k]) = ((__pyx_v_newFreqs[__pyx_v_k]) / ((double)(__pyx_v_self->ploidy * __pyx_v_nIndWithData))); /* "cpopulation.pyx":487 * for k from 0 <= k < self.nHaplotypes: * newFreqs[k] = newFreqs[k]/(self.ploidy*nIndWithData) * freqChange = fabs(freq[k] - newFreqs[k]) # <<<<<<<<<<<<<< * * if freqChange > maxChange: */ __pyx_v_freqChange = fabs(((__pyx_v_freq[__pyx_v_k]) - (__pyx_v_newFreqs[__pyx_v_k]))); /* "cpopulation.pyx":489 * freqChange = fabs(freq[k] - newFreqs[k]) * * if freqChange > maxChange: # <<<<<<<<<<<<<< * maxChange = freqChange * */ __pyx_t_2 = (__pyx_v_freqChange > __pyx_v_maxChange); if (__pyx_t_2) { /* "cpopulation.pyx":490 * * if freqChange > maxChange: * maxChange = freqChange # <<<<<<<<<<<<<< * * freq[k] = newFreqs[k] */ __pyx_v_maxChange = __pyx_v_freqChange; goto __pyx_L20; } __pyx_L20:; /* "cpopulation.pyx":492 * maxChange = freqChange * * freq[k] = newFreqs[k] # <<<<<<<<<<<<<< * * return maxChange */ (__pyx_v_freq[__pyx_v_k]) = (__pyx_v_newFreqs[__pyx_v_k]); } /* "cpopulation.pyx":494 * freq[k] = newFreqs[k] * * return maxChange # <<<<<<<<<<<<<< * * cdef double calculatePosterior(self, Variant var, int flatPrior=0): */ __pyx_r = __pyx_v_maxChange; 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CYTHON_UNUSED double __pyx_v_phredPosterior; double __pyx_v_sumProbVariantThisIndividual; double __pyx_v_sumProbNoVariantThisIndividual; double __pyx_v_sumLogProbVariant; double __pyx_v_sumLogProbNoVariant; double __pyx_v_r_prime; double __pyx_v_s_prime; double __pyx_v_factor; int __pyx_v_i; int __pyx_v_j; int __pyx_v_r; int __pyx_v_s; int __pyx_v_nReadsThisInd; int __pyx_v_logOfMinFloat; struct __pyx_obj_7cwindow_bamReadBuffer *__pyx_v_theBuffer = 0; double __pyx_r; __Pyx_RefNannyDeclarations double *__pyx_t_1; int __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; PyObject *__pyx_t_6 = NULL; int __pyx_t_7; PyObject *__pyx_t_8 = NULL; int __pyx_t_9; PyObject *__pyx_t_10 = NULL; PyObject *__pyx_t_11 = NULL; PyObject *__pyx_t_12 = NULL; PyObject *__pyx_t_13 = NULL; PyObject *__pyx_t_14 = NULL; double __pyx_t_15; double __pyx_t_16; double __pyx_t_17; long __pyx_t_18; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("calculatePosterior", 0); if (__pyx_optional_args) { if (__pyx_optional_args->__pyx_n > 0) { __pyx_v_flatPrior = __pyx_optional_args->flatPrior; } } /* "cpopulation.pyx":504 * cdef tuple vsf * cdef double* genotypeLikelihoodsThisIndividual * cdef double* freqsPrimeByHapIndex = self.freqsPrimeByHapIndex # <<<<<<<<<<<<<< * cdef double prior = 0.0 * */ __pyx_t_1 = __pyx_v_self->freqsPrimeByHapIndex; __pyx_v_freqsPrimeByHapIndex = __pyx_t_1; /* "cpopulation.pyx":505 * cdef double* genotypeLikelihoodsThisIndividual * cdef double* freqsPrimeByHapIndex = self.freqsPrimeByHapIndex * cdef double prior = 0.0 # <<<<<<<<<<<<<< * * if flatPrior == 1: */ __pyx_v_prior = 0.0; /* "cpopulation.pyx":507 * cdef double prior = 0.0 * * if flatPrior == 1: # <<<<<<<<<<<<<< * prior = 0.5 * else: */ __pyx_t_2 = (__pyx_v_flatPrior == 1); if (__pyx_t_2) { /* "cpopulation.pyx":508 * * if flatPrior == 1: * prior = 0.5 # <<<<<<<<<<<<<< * else: * prior = var.calculatePrior( self.refFile ) */ __pyx_v_prior = 0.5; goto __pyx_L3; } /*else*/ { /* "cpopulation.pyx":510 * prior = 0.5 * else: * prior = var.calculatePrior( self.refFile ) # <<<<<<<<<<<<<< * * cdef double totalProb = 0.0 */ __pyx_t_3 = ((PyObject *)__pyx_v_self->refFile); __Pyx_INCREF(__pyx_t_3); __pyx_v_prior = ((struct __pyx_vtabstruct_7variant_Variant *)__pyx_v_var->__pyx_vtab)->calculatePrior(__pyx_v_var, ((struct __pyx_obj_9fastafile_FastaFile *)__pyx_t_3)); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __pyx_L3:; /* "cpopulation.pyx":512 * prior = var.calculatePrior( self.refFile ) * * cdef double totalProb = 0.0 # <<<<<<<<<<<<<< * cdef double sumFreqs = 0.0 * cdef double thisFreq = 0.0 */ __pyx_v_totalProb = 0.0; /* "cpopulation.pyx":513 * * cdef double totalProb = 0.0 * cdef double sumFreqs = 0.0 # <<<<<<<<<<<<<< * cdef double thisFreq = 0.0 * cdef double ratio = 0.0 */ __pyx_v_sumFreqs = 0.0; /* "cpopulation.pyx":514 * cdef double totalProb = 0.0 * cdef double sumFreqs = 0.0 * cdef double thisFreq = 0.0 # <<<<<<<<<<<<<< * cdef double ratio = 0.0 * cdef double likelihoodThisGenotype = 0.0 */ __pyx_v_thisFreq = 0.0; /* "cpopulation.pyx":515 * cdef double sumFreqs = 0.0 * cdef double thisFreq = 0.0 * cdef double ratio = 0.0 # <<<<<<<<<<<<<< * cdef double likelihoodThisGenotype = 0.0 * cdef double variantPosterior = 0.0 */ __pyx_v_ratio = 0.0; /* "cpopulation.pyx":516 * cdef double thisFreq = 0.0 * cdef double ratio = 0.0 * cdef double likelihoodThisGenotype = 0.0 # <<<<<<<<<<<<<< * cdef double variantPosterior = 0.0 * cdef double phredPosterior = 0.0 */ __pyx_v_likelihoodThisGenotype = 0.0; /* "cpopulation.pyx":517 * cdef double ratio = 0.0 * cdef double likelihoodThisGenotype = 0.0 * cdef double variantPosterior = 0.0 # <<<<<<<<<<<<<< * cdef double phredPosterior = 0.0 * cdef double sumProbVariantThisIndividual = 0.0 */ __pyx_v_variantPosterior = 0.0; /* "cpopulation.pyx":518 * cdef double likelihoodThisGenotype = 0.0 * cdef double variantPosterior = 0.0 * cdef double phredPosterior = 0.0 # <<<<<<<<<<<<<< * cdef double sumProbVariantThisIndividual = 0.0 * cdef double sumProbNoVariantThisIndividual = 0.0 */ __pyx_v_phredPosterior = 0.0; /* "cpopulation.pyx":519 * cdef double variantPosterior = 0.0 * cdef double phredPosterior = 0.0 * cdef double sumProbVariantThisIndividual = 0.0 # <<<<<<<<<<<<<< * cdef double sumProbNoVariantThisIndividual = 0.0 * cdef double sumLogProbVariant = 0.0 */ __pyx_v_sumProbVariantThisIndividual = 0.0; /* "cpopulation.pyx":520 * cdef double phredPosterior = 0.0 * cdef double sumProbVariantThisIndividual = 0.0 * cdef double sumProbNoVariantThisIndividual = 0.0 # <<<<<<<<<<<<<< * cdef double sumLogProbVariant = 0.0 * cdef double sumLogProbNoVariant = 0.0 */ __pyx_v_sumProbNoVariantThisIndividual = 0.0; /* "cpopulation.pyx":521 * cdef double sumProbVariantThisIndividual = 0.0 * cdef double sumProbNoVariantThisIndividual = 0.0 * cdef double sumLogProbVariant = 0.0 # <<<<<<<<<<<<<< * cdef double sumLogProbNoVariant = 0.0 * cdef double r_prime = 0.0 */ __pyx_v_sumLogProbVariant = 0.0; /* "cpopulation.pyx":522 * cdef double sumProbNoVariantThisIndividual = 0.0 * cdef double sumLogProbVariant = 0.0 * cdef double sumLogProbNoVariant = 0.0 # <<<<<<<<<<<<<< * cdef double r_prime = 0.0 * cdef double s_prime = 0.0 */ __pyx_v_sumLogProbNoVariant = 0.0; /* "cpopulation.pyx":523 * cdef double sumLogProbVariant = 0.0 * cdef double sumLogProbNoVariant = 0.0 * cdef double r_prime = 0.0 # <<<<<<<<<<<<<< * cdef double s_prime = 0.0 * cdef double factor = 0.0 */ __pyx_v_r_prime = 0.0; /* "cpopulation.pyx":524 * cdef double sumLogProbNoVariant = 0.0 * cdef double r_prime = 0.0 * cdef double s_prime = 0.0 # <<<<<<<<<<<<<< * cdef double factor = 0.0 * cdef int i = 0 */ __pyx_v_s_prime = 0.0; /* "cpopulation.pyx":525 * cdef double r_prime = 0.0 * cdef double s_prime = 0.0 * cdef double factor = 0.0 # <<<<<<<<<<<<<< * cdef int i = 0 * cdef int j = 0 */ __pyx_v_factor = 0.0; /* "cpopulation.pyx":526 * cdef double s_prime = 0.0 * cdef double factor = 0.0 * cdef int i = 0 # <<<<<<<<<<<<<< * cdef int j = 0 * cdef int r = 0 */ __pyx_v_i = 0; /* "cpopulation.pyx":527 * cdef double factor = 0.0 * cdef int i = 0 * cdef int j = 0 # <<<<<<<<<<<<<< * cdef int r = 0 * cdef int s = 0 */ __pyx_v_j = 0; /* "cpopulation.pyx":528 * cdef int i = 0 * cdef int j = 0 * cdef int r = 0 # <<<<<<<<<<<<<< * cdef int s = 0 * cdef int nReadsThisInd = 0 */ __pyx_v_r = 0; /* "cpopulation.pyx":529 * cdef int j = 0 * cdef int r = 0 * cdef int s = 0 # <<<<<<<<<<<<<< * cdef int nReadsThisInd = 0 * cdef int logOfMinFloat = -708 */ __pyx_v_s = 0; /* "cpopulation.pyx":530 * cdef int r = 0 * cdef int s = 0 * cdef int nReadsThisInd = 0 # <<<<<<<<<<<<<< * cdef int logOfMinFloat = -708 * cdef bamReadBuffer theBuffer */ __pyx_v_nReadsThisInd = 0; /* "cpopulation.pyx":531 * cdef int s = 0 * cdef int nReadsThisInd = 0 * cdef int logOfMinFloat = -708 # <<<<<<<<<<<<<< * cdef bamReadBuffer theBuffer * */ __pyx_v_logOfMinFloat = -708; /* "cpopulation.pyx":534 * cdef bamReadBuffer theBuffer * * if self.verbosity >= 3: # <<<<<<<<<<<<<< * logger.debug("") * logger.debug("#########################################################################") */ __pyx_t_2 = (__pyx_v_self->verbosity >= 3); if (__pyx_t_2) { /* "cpopulation.pyx":535 * * if self.verbosity >= 3: * logger.debug("") # <<<<<<<<<<<<<< * logger.debug("#########################################################################") * logger.debug("Posterior calculation debug information") */ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); 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void *r = NULL; m = PyImport_ImportModule((char *)modname); if (!m) goto end; p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); if (!p) goto end; r = PyLong_AsVoidPtr(p); end: Py_XDECREF(p); Py_XDECREF(m); return (__Pyx_RefNannyAPIStruct *)r; } #endif /* CYTHON_REFNANNY */ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) { PyObject *result; result = PyObject_GetAttr(dict, name); if (!result) { if (dict != __pyx_b) { PyErr_Clear(); result = PyObject_GetAttr(__pyx_b, name); } if (!result) { PyErr_SetObject(PyExc_NameError, name); } } return result; } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); value = Py_None; } #endif PyErr_NormalizeException(&type, &value, &tb); } else { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (PyExceptionClass_Check(type)) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyEval_CallObject(type, args); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static 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 int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(local_type, local_value, local_tb); #endif return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { /* try package relative import first */ PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: Py_XDECREF(empty_list); Py_XDECREF(py_import); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE void __Pyx_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 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 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_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_ImportVoidPtr #define __PYX_HAVE_RT_ImportVoidPtr static int __Pyx_ImportVoidPtr(PyObject *module, const char *name, void **p, const char *sig) { PyObject *d = 0; PyObject *cobj = 0; d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); if (!d) goto bad; cobj = PyDict_GetItemString(d, name); if (!cobj) { PyErr_Format(PyExc_ImportError, "%s does not export expected C variable %s", PyModule_GetName(module), name); 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 variable %s.%s has wrong signature (expected %s, got %s)", PyModule_GetName(module), name, sig, PyCapsule_GetName(cobj)); goto bad; } *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 variable %s.%s has wrong signature (expected %s, got %s)", PyModule_GetName(module), name, sig, desc); goto bad; } *p = PyCObject_AsVoidPtr(cobj);} #endif if (!(*p)) goto bad; Py_DECREF(d); return 0; bad: Py_XDECREF(d); return -1; } #endif #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 */