X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fcvcf.c;fp=pysam%2Fcvcf.c;h=6caaba0f31ab3a5799815dde5fe7184962a471fb;hp=d194519d5e20e227a6c1d69ba9d9128e3f26b897;hb=920cc77ed26707a0d92f9e436121b61d84bde627;hpb=8ab946e230447a6fe686edabc5e3cfa445da1721 diff --git a/pysam/cvcf.c b/pysam/cvcf.c index d194519..6caaba0 100644 --- a/pysam/cvcf.c +++ b/pysam/cvcf.c @@ -1,11 +1,12 @@ -/* Generated by Cython 0.14.1 on Sat Oct 15 05:27:48 2011 */ +/* Generated by Cython 0.16 on Mon Nov 19 08:44:41 2012 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02040000 + #error Cython requires Python 2.4+. #else - #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -34,10 +35,22 @@ #define PY_LONG_LONG LONG_LONG #endif -#if PY_VERSION_HEX < 0x02040000 - #define METH_COEXIST 0 - #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type) - #define PyDict_Contains(d,o) PySequence_Contains(d,o) +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif + +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif + +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyCFunction_Call PyObject_Call +#else + #define __Pyx_PyCFunction_Call PyCFunction_Call #endif #if PY_VERSION_HEX < 0x02050000 @@ -46,10 +59,13 @@ #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) - #define PyInt_AsSsize_t(o) PyInt_AsLong(o) + #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) PyNumber_Int(o) #define PyIndex_Check(o) PyNumber_Check(o) #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) + #define __PYX_BUILD_PY_SSIZE_T "i" +#else + #define __PYX_BUILD_PY_SSIZE_T "n" #endif #if PY_VERSION_HEX < 0x02060000 @@ -83,13 +99,25 @@ #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 @@ -101,6 +129,17 @@ #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif + +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) +#endif + #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject @@ -159,13 +198,13 @@ #define PyBoolObject PyLongObject #endif - -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#if PY_VERSION_HEX < 0x03020000 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) @@ -209,16 +248,27 @@ #define __Pyx_DOCSTR(n) (n) #endif -#ifdef __cplusplus -#define __PYX_EXTERN_C extern "C" +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) #else -#define __PYX_EXTERN_C extern + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif #endif #if defined(WIN32) || defined(MS_WINDOWS) #define _USE_MATH_DEFINES #endif #include +#define __PYX_HAVE__cvcf #define __PYX_HAVE_API__cvcf #include "stdlib.h" #include "string.h" @@ -231,6 +281,9 @@ #include "unistd.h" #include "bgzf.h" #include "tabix.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS @@ -258,7 +311,7 @@ # else # define CYTHON_UNUSED # endif -# elif defined(__ICC) || defined(__INTEL_COMPILER) +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED @@ -273,6 +326,7 @@ typedef struct {PyObject **p; char *s; const long n; const char* encoding; const #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); @@ -282,20 +336,20 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) - +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ -/* Test for GCC > 2.95 */ -#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) -#define likely(x) __builtin_expect(!!(x), 1) -#define unlikely(x) __builtin_expect(!!(x), 0) -#else /* __GNUC__ > 2 ... */ -#define likely(x) (x) -#define unlikely(x) (x) -#endif /* __GNUC__ > 2 ... */ + /* Test for GCC > 2.95 */ + #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) + #else /* __GNUC__ > 2 ... */ + #define likely(x) (x) + #define unlikely(x) (x) + #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ -#define likely(x) (x) -#define unlikely(x) (x) + #define likely(x) (x) + #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; @@ -314,16 +368,86 @@ static const char *__pyx_f[] = { "TabProxies.pxd", }; -/* Type declarations */ +/*--- Type declarations ---*/ +struct __pyx_obj_6ctabix_Parser; +struct __pyx_obj_6ctabix_asVCF; +struct __pyx_obj_10TabProxies_TupleProxy; +struct __pyx_obj_10TabProxies_NamedTupleProxy; +struct __pyx_obj_10TabProxies_BedProxy; +struct __pyx_obj_6ctabix_tabix_copy_iterator; +struct __pyx_obj_4cvcf_VCFRecord; +struct __pyx_obj_10TabProxies_VCFProxy; +struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse; +struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data; +struct __pyx_obj_6ctabix_TabixIterator; +struct __pyx_obj_4cvcf_asVCFRecord; +struct __pyx_obj_10TabProxies_GTFProxy; +struct __pyx_obj_6ctabix_TabixIteratorParsed; +struct __pyx_obj_6ctabix_TabixHeaderIterator; +struct __pyx_obj_6ctabix_Tabixfile; +struct __pyx_obj_6ctabix_asGTF; +struct __pyx_obj_6ctabix_asBed; +struct __pyx_obj_6ctabix_tabix_inplace_iterator; +struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr; +struct __pyx_obj_6ctabix_asTuple; +struct __pyx_defaults; +typedef struct __pyx_defaults __pyx_defaults; +struct __pyx_defaults1; +typedef struct __pyx_defaults1 __pyx_defaults1; +struct __pyx_defaults2; +typedef struct __pyx_defaults2 __pyx_defaults2; +struct __pyx_defaults3; +typedef struct __pyx_defaults3 __pyx_defaults3; +struct __pyx_defaults4; +typedef struct __pyx_defaults4 __pyx_defaults4; +struct __pyx_defaults { + PyObject *__pyx_arg_leftalign; +}; +struct __pyx_defaults1 { + PyObject *__pyx_arg_filter; +}; +struct __pyx_defaults2 { + PyObject *__pyx_arg_filter; +}; +struct __pyx_defaults3 { + PyObject *__pyx_arg_key; + PyObject *__pyx_arg_value; +}; +struct __pyx_defaults4 { + PyObject *__pyx_arg_lineparse; +}; + +/* "ctabix.pxd":190 + * cdef tabix_t * tabixfile + * + * cdef class Parser: # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_6ctabix_Parser { + PyObject_HEAD +}; + + +/* "ctabix.pxd":202 + * pass + * + * cdef class asVCF(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_6ctabix_asVCF { + struct __pyx_obj_6ctabix_Parser __pyx_base; +}; + -/* "TabProxies.pxd":42 +/* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ - struct __pyx_obj_10TabProxies_TupleProxy { PyObject_HEAD struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab; @@ -336,26 +460,26 @@ struct __pyx_obj_10TabProxies_TupleProxy { int is_modified; }; -/* "TabProxies.pxd":77 - * cdef update( self, char * buffer, size_t nbytes ) + +/* "TabProxies.pxd":69 + * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ - struct __pyx_obj_10TabProxies_NamedTupleProxy { struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; }; -/* "TabProxies.pxd":80 + +/* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ - struct __pyx_obj_10TabProxies_BedProxy { struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base; char *contig; @@ -364,6 +488,22 @@ struct __pyx_obj_10TabProxies_BedProxy { int bedfields; }; + +/* "ctabix.pxd":218 + * cdef __cnext__(self) + * + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef Parser parser + */ +struct __pyx_obj_6ctabix_tabix_copy_iterator { + PyObject_HEAD + struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab; + FILE *infile; + struct __pyx_obj_6ctabix_Parser *parser; +}; + + /* "cvcf.pyx":94 * ########################################################################################################### * @@ -371,7 +511,6 @@ struct __pyx_obj_10TabProxies_BedProxy { * '''vcf record. * */ - struct __pyx_obj_4cvcf_VCFRecord { struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; PyObject *vcf; @@ -379,31 +518,80 @@ struct __pyx_obj_4cvcf_VCFRecord { uint32_t pos; }; -/* "TabProxies.pxd":91 + +/* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ - struct __pyx_obj_10TabProxies_VCFProxy { struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t pos; }; -/* "ctabix.pxd":178 - * cdef tabix_t * tabixfile + +/* "cvcf.pyx":899 + * return line * - * cdef class Parser: # <<<<<<<<<<<<<< - * pass + * def _parse(self, line, stream): # <<<<<<<<<<<<<< + * # deal with files with header only + * if line.startswith("##"): return + */ +struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse { + PyObject_HEAD + PyObject *__pyx_v_d; + PyObject *__pyx_v_line; + PyObject *__pyx_v_self; + PyObject *__pyx_v_stream; + Py_ssize_t __pyx_t_0; + PyObject *__pyx_t_1; + PyObject *(*__pyx_t_2)(PyObject *); +}; + + +/* "cvcf.pyx":647 + * return False + * + * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< + * cols = line.split('\t') + * if len(cols) != len(self._samples)+9: */ +struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data { + PyObject_HEAD + PyObject *__pyx_v_alt; +}; -struct __pyx_obj_6ctabix_Parser { + +/* "ctabix.pxd":182 + * cdef char * _filename + * + * cdef class TabixIterator: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile + */ +struct __pyx_obj_6ctabix_TabixIterator { PyObject_HEAD + ti_iter_t iterator; + tabix_t *tabixfile; +}; + + +/* "cvcf.pyx":226 + * + * + * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<< + * '''converts a :term:`tabix row` into a VCF record.''' + * cdef vcffile + */ +struct __pyx_obj_4cvcf_asVCFRecord { + struct __pyx_obj_6ctabix_Parser __pyx_base; + PyObject *vcffile; }; + /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * @@ -411,50 +599,143 @@ struct __pyx_obj_6ctabix_Parser { * * cdef: */ - struct __pyx_obj_10TabProxies_GTFProxy { struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; - char *contig; - char *source; - char *feature; - uint32_t start; - uint32_t end; - char *score; - char *strand; - char *frame; - char *attributes; + char *_attributes; int hasOwnAttributes; }; -/* "cvcf.pyx":221 - * + +/* "ctabix.pxd":205 + * pass * - * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<< - * '''converts a :term:`tabix row` into a VCF record.''' - * cdef vcffile + * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile */ +struct __pyx_obj_6ctabix_TabixIteratorParsed { + PyObject_HEAD + ti_iter_t iterator; + tabix_t *tabixfile; + struct __pyx_obj_6ctabix_Parser *parser; +}; -struct __pyx_obj_4cvcf_asVCFRecord { - struct __pyx_obj_6ctabix_Parser __pyx_base; - PyObject *vcffile; + +/* "ctabix.pxd":186 + * cdef tabix_t * tabixfile + * + * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile + */ +struct __pyx_obj_6ctabix_TabixHeaderIterator { + PyObject_HEAD + ti_iter_t iterator; + tabix_t *tabixfile; }; + /* "ctabix.pxd":172 * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) * * cdef class Tabixfile: # <<<<<<<<<<<<<< - * cdef char * filename * + * # pointer to tabixfile */ - struct __pyx_obj_6ctabix_Tabixfile { PyObject_HEAD - char *filename; tabix_t *tabixfile; + int isremote; + char *_filename; +}; + + +/* "ctabix.pxd":196 + * pass + * + * cdef class asGTF(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_6ctabix_asGTF { + struct __pyx_obj_6ctabix_Parser __pyx_base; +}; + + +/* "ctabix.pxd":199 + * pass + * + * cdef class asBed(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_6ctabix_asBed { + struct __pyx_obj_6ctabix_Parser __pyx_base; +}; + + +/* "ctabix.pxd":210 + * cdef Parser parser + * + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef char * buffer + */ +struct __pyx_obj_6ctabix_tabix_inplace_iterator { + PyObject_HEAD + struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab; + FILE *infile; + char *buffer; + size_t size; + struct __pyx_obj_6ctabix_Parser *parser; +}; + + +/* "cvcf.pyx":790 + * if alt: + * for i in range(1,min(len(ref),min(map(len,alt)))): + * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< + * break + * ref, alt = ref[:-1], [allele[:-1] for allele in alt] + */ +struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr { + PyObject_HEAD + struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope; + PyObject *__pyx_v_allele; + PyObject *__pyx_t_0; + Py_ssize_t __pyx_t_1; + PyObject *(*__pyx_t_2)(PyObject *); +}; + + +/* "ctabix.pxd":193 + * pass + * + * cdef class asTuple(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_6ctabix_asTuple { + struct __pyx_obj_6ctabix_Parser __pyx_base; +}; + + + +/* "ctabix.pxd":218 + * cdef __cnext__(self) + * + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef Parser parser + */ + +struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *); }; +static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator; -/* "TabProxies.pxd":42 +/* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< @@ -472,8 +753,8 @@ struct __pyx_vtabstruct_10TabProxies_TupleProxy { static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy; -/* "TabProxies.pxd":77 - * cdef update( self, char * buffer, size_t nbytes ) +/* "TabProxies.pxd":69 + * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass @@ -486,7 +767,7 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy { static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy; -/* "TabProxies.pxd":91 +/* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -500,6 +781,20 @@ struct __pyx_vtabstruct_10TabProxies_VCFProxy { static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy; +/* "ctabix.pxd":210 + * cdef Parser parser + * + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef char * buffer + */ + +struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *); +}; +static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator; + + /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * @@ -510,6 +805,7 @@ static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies struct __pyx_vtabstruct_10TabProxies_GTFProxy { struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; + char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *); }; static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy; @@ -528,7 +824,7 @@ struct __pyx_vtabstruct_4cvcf_VCFRecord { static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord; -/* "TabProxies.pxd":80 +/* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -540,11 +836,9 @@ struct __pyx_vtabstruct_10TabProxies_BedProxy { struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; }; static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy; - #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif - #if CYTHON_REFNANNY typedef struct { void (*INCREF)(void*, PyObject*, int); @@ -555,48 +849,57 @@ static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies void (*FinishContext)(void**); } __Pyx_RefNannyAPIStruct; static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; - static __Pyx_RefNannyAPIStruct * __Pyx_RefNannyImportAPI(const char *modname) { - PyObject *m = NULL, *p = NULL; - 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; - } - #define __Pyx_RefNannySetupContext(name) void *__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) - #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny) - #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) - #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) - #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/ + #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; +#ifdef WITH_THREAD + #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + if (acquire_gil) { \ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + PyGILState_Release(__pyx_gilstate_save); \ + } else { \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + } +#else + #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) +#endif + #define __Pyx_RefNannyFinishContext() \ + __Pyx_RefNanny->FinishContext(&__pyx_refnanny) + #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) + #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__) - #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r);} } while(0) + #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0) + #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0) + #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0) + #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) #else - #define __Pyx_RefNannySetupContext(name) + #define __Pyx_RefNannyDeclarations + #define __Pyx_RefNannySetupContext(name, acquire_gil) #define __Pyx_RefNannyFinishContext() #define __Pyx_INCREF(r) Py_INCREF(r) #define __Pyx_DECREF(r) Py_DECREF(r) #define __Pyx_GOTREF(r) #define __Pyx_GIVEREF(r) + #define __Pyx_XINCREF(r) Py_XINCREF(r) #define __Pyx_XDECREF(r) Py_XDECREF(r) + #define __Pyx_XGOTREF(r) + #define __Pyx_XGIVEREF(r) #endif /* CYTHON_REFNANNY */ -#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0) -#define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r);} } while(0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ -static void __Pyx_RaiseDoubleKeywordsError( - const char* func_name, PyObject* kw_name); /*proto*/ - -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); /*proto*/ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; @@ -605,12 +908,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j Py_DECREF(j); return r; } - - #define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_List_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { if (likely(o != Py_None)) { if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { @@ -626,11 +926,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_ } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } - #define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Tuple_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { if (likely(o != Py_None)) { if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { @@ -646,29 +944,33 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } - - #define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) { - PyObject *r; - if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) { - r = PyList_GET_ITEM(o, i); - Py_INCREF(r); - } - else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { - r = PyTuple_GET_ITEM(o, i); - Py_INCREF(r); + if (PyList_CheckExact(o)) { + Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } } - else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) { - r = PySequence_GetItem(o, i); + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } } - else { - r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); + else if (likely(i >= 0)) { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + return m->sq_item(o, i); + } } - return r; + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ @@ -676,13 +978,14 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ - #define __Pyx_PyObject_AsDouble(obj) \ - ((likely(PyFloat_CheckExact(obj))) ? \ - PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) +((likely(PyFloat_CheckExact(obj))) ? \ + PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void); @@ -706,7 +1009,9 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif -static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; } +static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) { + return unlikely(b < 0) ? b : !b; +} static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b); } @@ -715,8 +1020,7 @@ static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); -static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/ -static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/ +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ @@ -739,7 +1043,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { #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; @@ -747,135 +1050,128 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb Py_DECREF(j); return r; } - static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) { - if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) { - Py_INCREF(v); - Py_DECREF(PyList_GET_ITEM(o, i)); - PyList_SET_ITEM(o, i, v); - return 1; - } - else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && (likely(i >= 0))) - return PySequence_SetItem(o, i, v); - else { - PyObject *j = PyInt_FromSsize_t(i); - return __Pyx_SetItemInt_Generic(o, j, v); + 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 if (likely(i >= 0)) { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_ass_item)) { + return m->sq_ass_item(o, i, v); + } } + return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); } +static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname); + #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 */ -#if PY_VERSION_HEX < 0x02040000 -#ifndef Py_SETOBJECT_H -#define Py_SETOBJECT_H - -static PyTypeObject *__Pyx_PySet_Type = NULL; -static PyTypeObject *__Pyx_PyFrozenSet_Type = NULL; +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ -#define PySet_Type (*__Pyx_PySet_Type) -#define PyFrozenSet_Type (*__Pyx_PyFrozenSet_Type) +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/ -#define PyAnySet_Check(ob) \ - (PyAnySet_CheckExact(ob) || \ - PyType_IsSubtype((ob)->ob_type, &PySet_Type) || \ - PyType_IsSubtype((ob)->ob_type, &PyFrozenSet_Type)) +static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name); -#define PyFrozenSet_CheckExact(ob) ((ob)->ob_type == &PyFrozenSet_Type) - -static int __Pyx_Py23SetsImport(void) { - PyObject *sets=0, *Set=0, *ImmutableSet=0; - - sets = PyImport_ImportModule((char *)"sets"); - if (!sets) goto bad; - Set = PyObject_GetAttrString(sets, (char *)"Set"); - if (!Set) goto bad; - ImmutableSet = PyObject_GetAttrString(sets, (char *)"ImmutableSet"); - if (!ImmutableSet) goto bad; - Py_DECREF(sets); - - __Pyx_PySet_Type = (PyTypeObject*) Set; - __Pyx_PyFrozenSet_Type = (PyTypeObject*) ImmutableSet; - - return 0; - - bad: - Py_XDECREF(sets); - Py_XDECREF(Set); - Py_XDECREF(ImmutableSet); - return -1; -} - -#else -static int __Pyx_Py23SetsImport(void) { return 0; } -#endif /* !Py_SETOBJECT_H */ -#endif /* < Py2.4 */ -#endif /* < Py2.5 */ - -static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ -static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ - -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/ - -static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ +static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *modname); /*proto*/ -#define __pyx_binding_PyCFunctionType_USED 1 - +#define __Pyx_CyFunction_USED 1 +#include +#define __Pyx_CYFUNCTION_STATICMETHOD 0x01 +#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 +#define __Pyx_CYFUNCTION_CCLASS 0x04 +#define __Pyx_CyFunction_GetClosure(f) \ + (((__pyx_CyFunctionObject *) (f))->func_closure) +#define __Pyx_CyFunction_GetClassObj(f) \ + (((__pyx_CyFunctionObject *) (f))->func_classobj) +#define __Pyx_CyFunction_Defaults(type, f) \ + ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) +#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ + ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) typedef struct { PyCFunctionObject func; -} __pyx_binding_PyCFunctionType_object; + int flags; + PyObject *func_dict; + PyObject *func_weakreflist; + PyObject *func_name; + PyObject *func_doc; + PyObject *func_code; + PyObject *func_closure; + PyObject *func_classobj; /* No-args super() class cell */ + void *defaults; + int defaults_pyobjects; + PyObject *defaults_tuple; /* Const defaults tuple */ + PyObject *(*defaults_getter)(PyObject *); +} __pyx_CyFunctionObject; +static PyTypeObject *__pyx_CyFunctionType = 0; +#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \ + __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code) +static PyObject *__Pyx_CyFunction_New(PyTypeObject *, + PyMethodDef *ml, int flags, + PyObject *self, PyObject *module, + PyObject* code); +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, + size_t size, + int pyobjects); +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, + PyObject *tuple); +static int __Pyx_CyFunction_init(void); -static PyTypeObject __pyx_binding_PyCFunctionType_type; -static PyTypeObject *__pyx_binding_PyCFunctionType = NULL; +static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); -static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */ -#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL) +#include -static int __pyx_binding_PyCFunctionType_init(void); /* proto */ +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ -static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ + +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals +#else +#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals +#endif static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); @@ -909,7 +1205,38 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); -static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/ +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ + +#define __Pyx_Generator_USED +#include +typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); +typedef struct { + PyObject_HEAD + __pyx_generator_body_t body; + PyObject *closure; + int is_running; + int resume_label; + PyObject *exc_type; + PyObject *exc_value; + PyObject *exc_traceback; + PyObject *gi_weakreflist; + PyObject *classobj; +} __pyx_GeneratorObject; +static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, + PyObject *closure); +static int __pyx_Generator_init(void); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ @@ -917,39 +1244,133 @@ static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ -static void __Pyx_AddTraceback(const char *funcname); /*proto*/ +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ -/* Module declarations from ctabix */ + +/* Module declarations from 'ctabix' */ static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0; +static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0; +static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0; static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0; -/* Module declarations from TabProxies */ - +static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0; +static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0; +static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0; +static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0; +static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0; +static PyTypeObject *__pyx_ptype_6ctabix_tabix_inplace_iterator = 0; +static PyTypeObject *__pyx_ptype_6ctabix_tabix_copy_iterator = 0; + +/* Module declarations from 'TabProxies' */ static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0; static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0; static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0; static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0; static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0; -/* Module declarations from cvcf */ +/* Module declarations from 'cvcf' */ static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0; static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0; +static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct__parse_data = 0; +static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr = 0; +static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct_2__parse = 0; #define __Pyx_MODULE_NAME "cvcf" -static int __pyx_module_is_main_cvcf = 0; +int __pyx_module_is_main_cvcf = 0; -/* Implementation of cvcf */ +/* Implementation of 'cvcf' */ static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_min; -static PyObject *__pyx_builtin_len; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_NotImplementedError; +static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */ +static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */ +static int __pyx_pf_4cvcf_9VCFRecord___init__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ +static int __pyx_pf_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ +static Py_ssize_t __pyx_pf_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static int __pyx_pf_4cvcf_11asVCFRecord___init__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */ +static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ +static PyObject *__pyx_pf_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */ static char __pyx_k_1[] = ""; static char __pyx_k_2[] = ","; static char __pyx_k_4[] = ":"; @@ -962,124 +1383,167 @@ static char __pyx_k_18[] = "BAD_NUMBER_OF_VALUES"; static char __pyx_k_19[] = "(found %s values in element %s; expected %s)"; static char __pyx_k_20[] = "BAD_NUMBER_OF_PARAMETERS"; static char __pyx_k_21[] = "id=%s, expected %s parameters, got %s"; -static char __pyx_k_25[] = "Line %s: '%s'\n%s %s: %s\n"; -static char __pyx_k_27[] = "<"; -static char __pyx_k_29[] = "V40_MISSING_ANGLE_BRACKETS"; -static char __pyx_k_30[] = ">"; -static char __pyx_k_34[] = "\""; -static char __pyx_k_38[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS"; -static char __pyx_k_39[] = "BADLY_FORMATTED_FORMAT_STRING"; -static char __pyx_k_40[] = "ID="; -static char __pyx_k_41[] = "Number="; -static char __pyx_k_42[] = "Type="; -static char __pyx_k_43[] = "Description="; -static char __pyx_k_52[] = "FORMAT_MISSING_QUOTES"; -static char __pyx_k_55[] = ""; -static char __pyx_k_56[] = "#alleles"; -static char __pyx_k_57[] = "#nonref_alleles"; -static char __pyx_k_58[] = "#genotypes"; -static char __pyx_k_59[] = "#phased_genotypes"; -static char __pyx_k_61[] = "Unknown number type encountered: %s"; -static char __pyx_k_62[] = "%s=%s"; -static char __pyx_k_63[] = "(Undefined tag)"; -static char __pyx_k_66[] = "(output)"; -static char __pyx_k_69[] = "Genotype Quality"; -static char __pyx_k_70[] = "Read depth at this position for this sample"; +static char __pyx_k_24[] = " in line %s: '%s'\n%s %s: %s\n"; +static char __pyx_k_25[] = "<"; +static char __pyx_k_27[] = "V40_MISSING_ANGLE_BRACKETS"; +static char __pyx_k_28[] = ">"; +static char __pyx_k_32[] = "\""; +static char __pyx_k_36[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS"; +static char __pyx_k_37[] = "BADLY_FORMATTED_FORMAT_STRING"; +static char __pyx_k_38[] = "ID="; +static char __pyx_k_39[] = "Number="; +static char __pyx_k_40[] = "Type="; +static char __pyx_k_41[] = "Description="; +static char __pyx_k_50[] = "FORMAT_MISSING_QUOTES"; +static char __pyx_k_53[] = "#alleles"; +static char __pyx_k_54[] = "#nonref_alleles"; +static char __pyx_k_55[] = "#genotypes"; +static char __pyx_k_56[] = "#phased_genotypes"; +static char __pyx_k_57[] = "ZERO_FOR_NON_FLAG_FIELD"; +static char __pyx_k_58[] = "Unknown number type encountered: %s"; +static char __pyx_k_59[] = "%s=%s"; +static char __pyx_k_60[] = "(Undefined tag)"; +static char __pyx_k_61[] = "(output)"; +static char __pyx_k_64[] = "Read depth at this position for this sample"; +static char __pyx_k_65[] = "Sample Genotype Filter"; +static char __pyx_k_66[] = "Genotype likelihoods"; +static char __pyx_k_67[] = "Genotype Quality"; +static char __pyx_k_68[] = "Phred-scaled genotype likelihoods"; +static char __pyx_k_69[] = "Genotype posterior probabilities"; +static char __pyx_k_70[] = "Conditional genotype quality"; static char __pyx_k_71[] = "Haplotype Quality"; -static char __pyx_k_72[] = "Sample Genotype Filter"; -static char __pyx_k_73[] = "##"; -static char __pyx_k_76[] = "VCFv3.3"; -static char __pyx_k_77[] = "VCFv4.0"; -static char __pyx_k_78[] = "VCFv4.1"; -static char __pyx_k_79[] = "UNKNOWN_FORMAT_STRING"; -static char __pyx_k_80[] = "##fileformat=VCFv%s.%s\n"; -static char __pyx_k_81[] = "##%s=%s\n"; -static char __pyx_k_82[] = "#"; -static char __pyx_k_85[] = "\t"; -static char __pyx_k_87[] = "HEADING_NOT_SEPARATED_BY_TABS"; -static char __pyx_k_88[] = "(%sth entry not found)"; -static char __pyx_k_89[] = "(found %s, expected %s)"; -static char __pyx_k_90[] = "BADLY_FORMATTED_HEADING"; -static char __pyx_k_91[] = "\n"; -static char __pyx_k_92[] = "|"; -static char __pyx_k_93[] = "ERROR_FLAG_HAS_VALUE"; -static char __pyx_k_97[] = "ERROR_FORMAT_NOT_NUMERICAL"; -static char __pyx_k_98[] = "ERROR_FORMAT_NOT_CHAR"; +static char __pyx_k_72[] = "Phase set"; +static char __pyx_k_73[] = "Phasing quality"; +static char __pyx_k_74[] = "Expected alternate allel counts"; +static char __pyx_k_75[] = "RMS mapping quality"; +static char __pyx_k_76[] = "##"; +static char __pyx_k_79[] = "VCFv3.3"; +static char __pyx_k_80[] = "VCFv4.0"; +static char __pyx_k_81[] = "VCFv4.1"; +static char __pyx_k_82[] = "UNKNOWN_FORMAT_STRING"; +static char __pyx_k_83[] = "##fileformat=VCFv%s.%s\n"; +static char __pyx_k_84[] = "##%s=%s\n"; +static char __pyx_k_85[] = "#"; +static char __pyx_k_88[] = "\t"; +static char __pyx_k_90[] = "HEADING_NOT_SEPARATED_BY_TABS"; +static char __pyx_k_91[] = "(%sth entry not found)"; +static char __pyx_k_92[] = "(found %s, expected %s)"; +static char __pyx_k_93[] = "BADLY_FORMATTED_HEADING"; +static char __pyx_k_94[] = "\n"; +static char __pyx_k_95[] = "|"; +static char __pyx_k_96[] = "ERROR_FLAG_HAS_VALUE"; static char __pyx_k__0[] = "0"; +static char __pyx_k__A[] = "A"; static char __pyx_k__D[] = "D"; +static char __pyx_k__G[] = "G"; static char __pyx_k__I[] = "I"; static char __pyx_k__N[] = "N"; -static char __pyx_k_101[] = "BAD_NUMBER_OF_COLUMNS"; -static char __pyx_k_102[] = "expected %s for %s samples (%s), got %s"; -static char __pyx_k_103[] = "(reference is %s, VCF says %s)"; -static char __pyx_k_111[] = "V33_UNMATCHED_DELETION"; -static char __pyx_k_112[] = "(deletion is %s, reference is %s)"; -static char __pyx_k_113[] = "MISSING_INDEL_ALLELE_REF_BASE"; -static char __pyx_k_115[] = "Required key %s not found in data"; -static char __pyx_k_118[] = "enter_default_format"; -static char __pyx_k_119[] = "Can only handle v3.3 and v4.0 VCF files"; -static char __pyx_k_121[] = "Invalid error string: %s"; -static char __pyx_k_122[] = "needs to be checked"; -static char __pyx_k_126[] = "[|/\\\\]"; -static char __pyx_k_128[] = "^[ACGTN]+$"; -static char __pyx_k_130[] = "id numbertype number type description missingvalue"; -static char __pyx_k_132[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; -static char __pyx_k_133[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; -static char __pyx_k_134[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s"; -static char __pyx_k_135[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)"; -static char __pyx_k_136[] = "POS_NOT_NUMERICAL:Position column is not numerical"; -static char __pyx_k_137[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field"; -static char __pyx_k_138[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF"; -static char __pyx_k_139[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF"; -static char __pyx_k_140[] = "POS_NOT_POSITIVE:Position field must be >0"; -static char __pyx_k_141[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'"; -static char __pyx_k_142[] = "ERROR_INFO_STRING:Error while parsing info field"; -static char __pyx_k_143[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)"; -static char __pyx_k_144[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s"; -static char __pyx_k_145[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string"; -static char __pyx_k_146[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header"; -static char __pyx_k_147[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header"; -static char __pyx_k_148[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)"; -static char __pyx_k_149[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)"; -static char __pyx_k_150[] = "BAD_GENOTYPE:Cannot parse genotype (%s)"; -static char __pyx_k_151[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)"; -static char __pyx_k_152[] = "MISSING_REF:Reference allele missing"; -static char __pyx_k_153[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)"; -static char __pyx_k_154[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets"; -static char __pyx_k_155[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes"; -static char __pyx_k_156[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields"; -static char __pyx_k_157[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs"; -static char __pyx_k_158[] = "WRONG_REF:Wrong reference %s"; -static char __pyx_k_159[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data"; -static char __pyx_k_160[] = "BAD_CHR_TAG:Error calculating chr tag for %s"; -static char __pyx_k_161[] = "ZERO_LENGTH_ALLELE:Found zero-length allele"; -static char __pyx_k_162[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"; +static char __pyx_k__a[] = "a"; +static char __pyx_k__c[] = "c"; +static char __pyx_k__d[] = "d"; +static char __pyx_k__f[] = "f"; +static char __pyx_k__i[] = "i"; +static char __pyx_k__k[] = "k"; +static char __pyx_k__l[] = "l"; +static char __pyx_k__n[] = "n"; +static char __pyx_k__r[] = "r"; +static char __pyx_k__s[] = "s"; +static char __pyx_k__t[] = "t"; +static char __pyx_k__v[] = "v"; +static char __pyx_k__x[] = "x"; +static char __pyx_k__y[] = "y"; +static char __pyx_k_100[] = "ERROR_FORMAT_NOT_INTEGER"; +static char __pyx_k_101[] = "ERROR_FORMAT_NOT_CHAR"; +static char __pyx_k_102[] = "ERROR_FORMAT_NOT_NUMERICAL"; +static char __pyx_k_104[] = "BAD_NUMBER_OF_COLUMNS"; +static char __pyx_k_105[] = "expected %s for %s samples (%s), got %s"; +static char __pyx_k_106[] = "(reference is %s, VCF says %s)"; +static char __pyx_k_114[] = "V33_UNMATCHED_DELETION"; +static char __pyx_k_115[] = "(deletion is %s, reference is %s)"; +static char __pyx_k_116[] = "MISSING_INDEL_ALLELE_REF_BASE"; +static char __pyx_k_118[] = "Required key %s not found in data"; +static char __pyx_k_121[] = "enter_default_format"; +static char __pyx_k_123[] = "Can only handle v3.3 and v4.0 VCF files"; +static char __pyx_k_125[] = "Invalid error string: %s"; +static char __pyx_k_126[] = "needs to be checked"; +static char __pyx_k_128[] = "[|/\\\\]"; +static char __pyx_k_130[] = "^[ACGTN]+$"; +static char __pyx_k_134[] = "/ifs/devel/pysam/pysam/cvcf.pyx"; +static char __pyx_k_137[] = "id numbertype number type description missingvalue"; +static char __pyx_k_139[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; +static char __pyx_k_140[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; +static char __pyx_k_141[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s"; +static char __pyx_k_142[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)"; +static char __pyx_k_143[] = "POS_NOT_NUMERICAL:Position column is not numerical"; +static char __pyx_k_144[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field"; +static char __pyx_k_145[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF"; +static char __pyx_k_146[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF"; +static char __pyx_k_147[] = "POS_NOT_POSITIVE:Position field must be >0"; +static char __pyx_k_148[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'"; +static char __pyx_k_149[] = "ERROR_INFO_STRING:Error while parsing info field"; +static char __pyx_k_150[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)"; +static char __pyx_k_151[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s"; +static char __pyx_k_152[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string"; +static char __pyx_k_153[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header"; +static char __pyx_k_154[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header"; +static char __pyx_k_155[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)"; +static char __pyx_k_156[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)"; +static char __pyx_k_157[] = "BAD_GENOTYPE:Cannot parse genotype (%s)"; +static char __pyx_k_158[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)"; +static char __pyx_k_159[] = "MISSING_REF:Reference allele missing"; +static char __pyx_k_160[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)"; +static char __pyx_k_161[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets"; +static char __pyx_k_162[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes"; +static char __pyx_k_163[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields"; +static char __pyx_k_164[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs"; +static char __pyx_k_165[] = "WRONG_REF:Wrong reference %s"; +static char __pyx_k_166[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data"; +static char __pyx_k_167[] = "BAD_CHR_TAG:Error calculating chr tag for %s"; +static char __pyx_k_168[] = "ZERO_LENGTH_ALLELE:Found zero-length allele"; +static char __pyx_k_169[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"; +static char __pyx_k_170[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'"; +static char __pyx_k_171[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s"; +static char __pyx_k_172[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value"; static char __pyx_k__DP[] = "DP"; +static char __pyx_k__EC[] = "EC"; static char __pyx_k__FT[] = "FT"; +static char __pyx_k__GL[] = "GL"; +static char __pyx_k__GP[] = "GP"; static char __pyx_k__GQ[] = "GQ"; static char __pyx_k__GT[] = "GT"; static char __pyx_k__HQ[] = "HQ"; static char __pyx_k__ID[] = "ID"; +static char __pyx_k__MQ[] = "MQ"; +static char __pyx_k__PL[] = "PL"; +static char __pyx_k__PQ[] = "PQ"; +static char __pyx_k__PS[] = "PS"; static char __pyx_k__fa[] = "fa"; static char __pyx_k__id[] = "id"; +static char __pyx_k__na[] = "na"; static char __pyx_k__re[] = "re"; static char __pyx_k__ALT[] = "ALT"; +static char __pyx_k__GLE[] = "GLE"; static char __pyx_k__POS[] = "POS"; static char __pyx_k__REF[] = "REF"; static char __pyx_k__VCF[] = "VCF"; static char __pyx_k__add[] = "add"; static char __pyx_k__alt[] = "alt"; static char __pyx_k__end[] = "end"; +static char __pyx_k__err[] = "err"; static char __pyx_k__fmt[] = "fmt"; static char __pyx_k__get[] = "get"; +static char __pyx_k__gts[] = "gts"; +static char __pyx_k__idx[] = "idx"; static char __pyx_k__key[] = "key"; static char __pyx_k__len[] = "len"; static char __pyx_k__map[] = "map"; static char __pyx_k__min[] = "min"; +static char __pyx_k__nmb[] = "nmb"; static char __pyx_k__opt[] = "opt"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__ref[] = "ref"; static char __pyx_k__sys[] = "sys"; +static char __pyx_k__var[] = "var"; static char __pyx_k__vcf[] = "vcf"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__Flag[] = "Flag"; @@ -1087,21 +1551,28 @@ static char __pyx_k__INFO[] = "INFO"; static char __pyx_k__PASS[] = "PASS"; static char __pyx_k__QUAL[] = "QUAL"; static char __pyx_k__Type[] = "Type"; +static char __pyx_k__addn[] = "addn"; static char __pyx_k__alt1[] = "alt1"; static char __pyx_k__alt2[] = "alt2"; +static char __pyx_k__cols[] = "cols"; static char __pyx_k__copy[] = "copy"; static char __pyx_k__cvcf[] = "cvcf"; static char __pyx_k__data[] = "data"; +static char __pyx_k__dict[] = "dict"; +static char __pyx_k__elts[] = "elts"; static char __pyx_k__find[] = "find"; static char __pyx_k__info[] = "info"; static char __pyx_k__join[] = "join"; static char __pyx_k__keys[] = "keys"; +static char __pyx_k__last[] = "last"; +static char __pyx_k__left[] = "left"; static char __pyx_k__line[] = "line"; static char __pyx_k__pos1[] = "pos1"; static char __pyx_k__pos2[] = "pos2"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__ref1[] = "ref1"; static char __pyx_k__ref2[] = "ref2"; +static char __pyx_k__rest[] = "rest"; static char __pyx_k__self[] = "self"; static char __pyx_k__type[] = "type"; static char __pyx_k__ACGTN[] = "ACGTN"; @@ -1111,15 +1582,22 @@ static char __pyx_k__Float[] = "Float"; static char __pyx_k___copy[] = "_copy"; static char __pyx_k___info[] = "_info"; static char __pyx_k___line[] = "_line"; +static char __pyx_k__addns[] = "addns"; +static char __pyx_k__blurp[] = "blurp"; static char __pyx_k__chrom[] = "chrom"; static char __pyx_k__descr[] = "descr"; static char __pyx_k__error[] = "error"; +static char __pyx_k__faref[] = "faref"; static char __pyx_k__fetch[] = "fetch"; +static char __pyx_k__first[] = "first"; +static char __pyx_k__ielts[] = "ielts"; +static char __pyx_k__label[] = "label"; static char __pyx_k__lines[] = "lines"; static char __pyx_k__match[] = "match"; static char __pyx_k__parse[] = "parse"; static char __pyx_k__pysam[] = "pysam"; static char __pyx_k__range[] = "range"; +static char __pyx_k__sdata[] = "sdata"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; @@ -1133,22 +1611,23 @@ static char __pyx_k__Number[] = "Number"; static char __pyx_k__String[] = "String"; static char __pyx_k___lines[] = "_lines"; static char __pyx_k___parse[] = "_parse"; -static char __pyx_k__append[] = "append"; +static char __pyx_k__allele[] = "allele"; static char __pyx_k__bisect[] = "bisect"; static char __pyx_k__buffer[] = "buffer"; -static char __pyx_k__contig[] = "contig"; -static char __pyx_k__fields[] = "fields"; static char __pyx_k__filter[] = "filter"; static char __pyx_k__format[] = "format"; static char __pyx_k__header[] = "header"; static char __pyx_k__number[] = "number"; static char __pyx_k__object[] = "object"; -static char __pyx_k__offset[] = "offset"; +static char __pyx_k__output[] = "output"; static char __pyx_k__parser[] = "parser"; static char __pyx_k__record[] = "record"; static char __pyx_k__region[] = "region"; -static char __pyx_k__stderr[] = "stderr"; +static char __pyx_k__result[] = "result"; +static char __pyx_k__sample[] = "sample"; static char __pyx_k__stream[] = "stream"; +static char __pyx_k__string[] = "string"; +static char __pyx_k__values[] = "values"; static char __pyx_k__Integer[] = "Integer"; static char __pyx_k__Warning[] = "Warning"; static char __pyx_k____all__[] = "__all__"; @@ -1159,9 +1638,13 @@ static char __pyx_k___header[] = "_header"; static char __pyx_k___lineno[] = "_lineno"; static char __pyx_k__compile[] = "compile"; static char __pyx_k__connect[] = "connect"; +static char __pyx_k__errwarn[] = "errwarn"; +static char __pyx_k__genexpr[] = "genexpr"; static char __pyx_k__getinfo[] = "getinfo"; +static char __pyx_k__longest[] = "longest"; static char __pyx_k__missing[] = "missing"; -static char __pyx_k__nfields[] = "nfields"; +static char __pyx_k__movable[] = "movable"; +static char __pyx_k__newalts[] = "newalts"; static char __pyx_k__regions[] = "regions"; static char __pyx_k__replace[] = "replace"; static char __pyx_k__samples[] = "samples"; @@ -1180,10 +1663,15 @@ static char __pyx_k___samples[] = "_samples"; static char __pyx_k___version[] = "_version"; static char __pyx_k__deepcopy[] = "deepcopy"; static char __pyx_k__endswith[] = "endswith"; +static char __pyx_k__expected[] = "expected"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__gtsRegEx[] = "gtsRegEx"; +static char __pyx_k__headings[] = "headings"; static char __pyx_k__inregion[] = "inregion"; static char __pyx_k__operator[] = "operator"; +static char __pyx_k__required[] = "required"; +static char __pyx_k__sequence[] = "sequence"; +static char __pyx_k__shortest[] = "shortest"; static char __pyx_k__validate[] = "validate"; static char __pyx_k__Character[] = "Character"; static char __pyx_k__NT_NUMBER[] = "NT_NUMBER"; @@ -1196,6 +1684,7 @@ static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__getfilter[] = "getfilter"; static char __pyx_k__getformat[] = "getformat"; static char __pyx_k__getheader[] = "getheader"; +static char __pyx_k__last_line[] = "last_line"; static char __pyx_k__leftalign[] = "leftalign"; static char __pyx_k__lineparse[] = "lineparse"; static char __pyx_k__reference[] = "reference"; @@ -1210,6 +1699,7 @@ static char __pyx_k__NT_UNKNOWN[] = "NT_UNKNOWN"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k___leftalign[] = "_leftalign"; static char __pyx_k___reference[] = "_reference"; +static char __pyx_k__errorlabel[] = "errorlabel"; static char __pyx_k__fileformat[] = "fileformat"; static char __pyx_k__formatdict[] = "formatdict"; static char __pyx_k__getsamples[] = "getsamples"; @@ -1256,8 +1746,10 @@ static char __pyx_k__write_heading[] = "write_heading"; static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE"; static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE"; static char __pyx_k___sample2column[] = "_sample2column"; +static char __pyx_k__have_deletions[] = "have_deletions"; static char __pyx_k___add_definition[] = "_add_definition"; static char __pyx_k___ignored_errors[] = "_ignored_errors"; +static char __pyx_k__faref_leftflank[] = "faref_leftflank"; static char __pyx_k__POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE"; static char __pyx_k__parse_formatdata[] = "parse_formatdata"; static char __pyx_k__ERROR_INFO_STRING[] = "ERROR_INFO_STRING"; @@ -1273,28 +1765,25 @@ static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF"; static PyObject *__pyx_kp_s_1; +static PyObject *__pyx_n_s_100; static PyObject *__pyx_n_s_101; -static PyObject *__pyx_kp_s_102; -static PyObject *__pyx_kp_s_103; +static PyObject *__pyx_n_s_102; +static PyObject *__pyx_n_s_104; +static PyObject *__pyx_kp_s_105; +static PyObject *__pyx_kp_s_106; static PyObject *__pyx_kp_s_11; -static PyObject *__pyx_n_s_111; -static PyObject *__pyx_kp_s_112; -static PyObject *__pyx_n_s_113; +static PyObject *__pyx_n_s_114; static PyObject *__pyx_kp_s_115; -static PyObject *__pyx_n_s_118; -static PyObject *__pyx_kp_s_119; -static PyObject *__pyx_kp_s_121; -static PyObject *__pyx_kp_s_122; +static PyObject *__pyx_n_s_116; +static PyObject *__pyx_kp_s_118; +static PyObject *__pyx_n_s_121; +static PyObject *__pyx_kp_s_123; +static PyObject *__pyx_kp_s_125; static PyObject *__pyx_kp_s_126; static PyObject *__pyx_kp_s_128; static PyObject *__pyx_kp_s_130; -static PyObject *__pyx_kp_s_132; -static PyObject *__pyx_kp_s_133; static PyObject *__pyx_kp_s_134; -static PyObject *__pyx_kp_s_135; -static PyObject *__pyx_kp_s_136; static PyObject *__pyx_kp_s_137; -static PyObject *__pyx_kp_s_138; static PyObject *__pyx_kp_s_139; static PyObject *__pyx_kp_s_14; static PyObject *__pyx_kp_s_140; @@ -1320,61 +1809,78 @@ static PyObject *__pyx_kp_s_159; static PyObject *__pyx_kp_s_160; static PyObject *__pyx_kp_s_161; static PyObject *__pyx_kp_s_162; +static PyObject *__pyx_kp_s_163; +static PyObject *__pyx_kp_s_164; +static PyObject *__pyx_kp_s_165; +static PyObject *__pyx_kp_s_166; +static PyObject *__pyx_kp_s_167; +static PyObject *__pyx_kp_s_168; +static PyObject *__pyx_kp_s_169; +static PyObject *__pyx_kp_s_170; +static PyObject *__pyx_kp_s_171; +static PyObject *__pyx_kp_s_172; static PyObject *__pyx_n_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_2; static PyObject *__pyx_n_s_20; static PyObject *__pyx_kp_s_21; +static PyObject *__pyx_kp_s_24; static PyObject *__pyx_kp_s_25; -static PyObject *__pyx_kp_s_27; -static PyObject *__pyx_n_s_29; -static PyObject *__pyx_kp_s_30; -static PyObject *__pyx_kp_s_34; -static PyObject *__pyx_n_s_38; -static PyObject *__pyx_n_s_39; +static PyObject *__pyx_n_s_27; +static PyObject *__pyx_kp_s_28; +static PyObject *__pyx_kp_s_32; +static PyObject *__pyx_n_s_36; +static PyObject *__pyx_n_s_37; +static PyObject *__pyx_kp_s_38; +static PyObject *__pyx_kp_s_39; static PyObject *__pyx_kp_s_4; static PyObject *__pyx_kp_s_40; static PyObject *__pyx_kp_s_41; -static PyObject *__pyx_kp_s_42; -static PyObject *__pyx_kp_s_43; -static PyObject *__pyx_n_s_52; +static PyObject *__pyx_n_s_50; +static PyObject *__pyx_kp_s_53; +static PyObject *__pyx_kp_s_54; static PyObject *__pyx_kp_s_55; static PyObject *__pyx_kp_s_56; -static PyObject *__pyx_kp_s_57; +static PyObject *__pyx_n_s_57; static PyObject *__pyx_kp_s_58; static PyObject *__pyx_kp_s_59; static PyObject *__pyx_kp_s_6; +static PyObject *__pyx_kp_s_60; static PyObject *__pyx_kp_s_61; -static PyObject *__pyx_kp_s_62; -static PyObject *__pyx_kp_s_63; +static PyObject *__pyx_kp_s_64; +static PyObject *__pyx_kp_s_65; static PyObject *__pyx_kp_s_66; +static PyObject *__pyx_kp_s_67; +static PyObject *__pyx_kp_s_68; static PyObject *__pyx_kp_s_69; static PyObject *__pyx_kp_s_70; static PyObject *__pyx_kp_s_71; static PyObject *__pyx_kp_s_72; static PyObject *__pyx_kp_s_73; +static PyObject *__pyx_kp_s_74; +static PyObject *__pyx_kp_s_75; static PyObject *__pyx_kp_s_76; -static PyObject *__pyx_kp_s_77; -static PyObject *__pyx_kp_s_78; -static PyObject *__pyx_n_s_79; +static PyObject *__pyx_kp_s_79; static PyObject *__pyx_kp_s_8; static PyObject *__pyx_kp_s_80; static PyObject *__pyx_kp_s_81; -static PyObject *__pyx_kp_s_82; +static PyObject *__pyx_n_s_82; +static PyObject *__pyx_kp_s_83; +static PyObject *__pyx_kp_s_84; static PyObject *__pyx_kp_s_85; -static PyObject *__pyx_n_s_87; static PyObject *__pyx_kp_s_88; -static PyObject *__pyx_kp_s_89; static PyObject *__pyx_kp_b_9; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_n_s_90; static PyObject *__pyx_kp_s_91; static PyObject *__pyx_kp_s_92; static PyObject *__pyx_n_s_93; -static PyObject *__pyx_n_s_97; -static PyObject *__pyx_n_s_98; +static PyObject *__pyx_kp_s_94; +static PyObject *__pyx_kp_s_95; +static PyObject *__pyx_n_s_96; static PyObject *__pyx_kp_b__0; static PyObject *__pyx_kp_s__0; +static PyObject *__pyx_n_s__A; static PyObject *__pyx_n_s__ACGTN; static PyObject *__pyx_n_s__ALT; static PyObject *__pyx_n_s__BAD_GENOTYPE; @@ -1383,6 +1889,7 @@ static PyObject *__pyx_n_s__Character; static PyObject *__pyx_n_s__D; static PyObject *__pyx_n_s__DP; static PyObject *__pyx_n_s__Description; +static PyObject *__pyx_n_s__EC; static PyObject *__pyx_n_s__ERROR_INFO_STRING; static PyObject *__pyx_n_s__ERROR_TRAILING_DATA; static PyObject *__pyx_n_s__ERROR_UNKNOWN_KEY; @@ -1394,6 +1901,10 @@ static PyObject *__pyx_n_s__FORMAT_NOT_DEFINED; static PyObject *__pyx_n_s__FT; static PyObject *__pyx_n_s__Flag; static PyObject *__pyx_n_s__Float; +static PyObject *__pyx_n_s__G; +static PyObject *__pyx_n_s__GL; +static PyObject *__pyx_n_s__GLE; +static PyObject *__pyx_n_s__GP; static PyObject *__pyx_n_s__GQ; static PyObject *__pyx_n_s__GT; static PyObject *__pyx_n_s__GTdata; @@ -1406,6 +1917,7 @@ static PyObject *__pyx_n_s__INFO; static PyObject *__pyx_n_s__Integer; static PyObject *__pyx_n_s__KeyError; static PyObject *__pyx_n_s__MISSING_REF; +static PyObject *__pyx_n_s__MQ; static PyObject *__pyx_n_s__N; static PyObject *__pyx_n_s__NT_ALLELES; static PyObject *__pyx_n_s__NT_GENOTYPES; @@ -1417,9 +1929,12 @@ static PyObject *__pyx_n_s__NotImplementedError; static PyObject *__pyx_n_s__Number; static PyObject *__pyx_n_b__PASS; static PyObject *__pyx_n_s__PASS; +static PyObject *__pyx_n_s__PL; static PyObject *__pyx_n_s__POS; static PyObject *__pyx_n_s__POS_NOT_NUMERICAL; static PyObject *__pyx_n_s__POS_NOT_POSITIVE; +static PyObject *__pyx_n_s__PQ; +static PyObject *__pyx_n_s__PS; static PyObject *__pyx_n_s__QUAL; static PyObject *__pyx_n_s__QUAL_NOT_NUMERICAL; static PyObject *__pyx_n_s__REF; @@ -1463,47 +1978,63 @@ static PyObject *__pyx_n_s___sample2column; static PyObject *__pyx_n_s___samples; static PyObject *__pyx_n_s___version; static PyObject *__pyx_n_s___warn_errors; +static PyObject *__pyx_n_s__a; static PyObject *__pyx_n_s__add; +static PyObject *__pyx_n_s__addn; +static PyObject *__pyx_n_s__addns; +static PyObject *__pyx_n_s__allele; static PyObject *__pyx_n_s__alleleRegEx; static PyObject *__pyx_n_s__alt; static PyObject *__pyx_n_s__alt1; static PyObject *__pyx_n_s__alt2; -static PyObject *__pyx_n_s__append; static PyObject *__pyx_n_s__bisect; +static PyObject *__pyx_n_s__blurp; static PyObject *__pyx_n_s__buffer; +static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__chrom; static PyObject *__pyx_n_s__collections; +static PyObject *__pyx_n_s__cols; static PyObject *__pyx_n_s__compare_calls; static PyObject *__pyx_n_s__compile; static PyObject *__pyx_n_s__connect; -static PyObject *__pyx_n_s__contig; static PyObject *__pyx_n_s__convertGT; static PyObject *__pyx_n_s__convertGTback; static PyObject *__pyx_n_s__copy; static PyObject *__pyx_n_s__cvcf; +static PyObject *__pyx_n_s__d; static PyObject *__pyx_n_s__data; static PyObject *__pyx_n_s__datagenerator; static PyObject *__pyx_n_s__deepcopy; static PyObject *__pyx_n_s__defaultdict; static PyObject *__pyx_n_s__descr; static PyObject *__pyx_n_s__description; +static PyObject *__pyx_n_s__dict; +static PyObject *__pyx_n_s__elts; static PyObject *__pyx_n_s__end; static PyObject *__pyx_n_s__endswith; static PyObject *__pyx_n_s__enumerate; +static PyObject *__pyx_n_s__err; static PyObject *__pyx_n_s__error; +static PyObject *__pyx_n_s__errorlabel; static PyObject *__pyx_n_s__errorstring; +static PyObject *__pyx_n_s__errwarn; +static PyObject *__pyx_n_s__expected; +static PyObject *__pyx_n_s__f; static PyObject *__pyx_n_s__fa; +static PyObject *__pyx_n_s__faref; +static PyObject *__pyx_n_s__faref_leftflank; static PyObject *__pyx_n_s__fetch; -static PyObject *__pyx_n_s__fields; static PyObject *__pyx_n_s__fileformat; static PyObject *__pyx_n_s__filename; static PyObject *__pyx_n_s__filter; static PyObject *__pyx_n_s__find; +static PyObject *__pyx_n_s__first; static PyObject *__pyx_n_s__fmt; static PyObject *__pyx_n_s__format; static PyObject *__pyx_n_s__format_format; static PyObject *__pyx_n_s__format_formatdata; static PyObject *__pyx_n_s__formatdict; +static PyObject *__pyx_n_s__genexpr; static PyObject *__pyx_n_s__get; static PyObject *__pyx_n_s__get_expected; static PyObject *__pyx_n_s__get_sequence; @@ -1512,35 +2043,52 @@ static PyObject *__pyx_n_s__getformat; static PyObject *__pyx_n_s__getheader; static PyObject *__pyx_n_s__getinfo; static PyObject *__pyx_n_s__getsamples; +static PyObject *__pyx_n_s__gts; static PyObject *__pyx_n_s__gtsRegEx; +static PyObject *__pyx_n_s__have_deletions; static PyObject *__pyx_n_s__header; +static PyObject *__pyx_n_s__headings; +static PyObject *__pyx_n_s__i; static PyObject *__pyx_n_s__id; +static PyObject *__pyx_n_s__idx; +static PyObject *__pyx_n_s__ielts; static PyObject *__pyx_n_s__ignoreerror; static PyObject *__pyx_n_s__info; static PyObject *__pyx_n_s__inregion; static PyObject *__pyx_n_s__itemgetter; static PyObject *__pyx_n_s__itervalues; static PyObject *__pyx_n_s__join; +static PyObject *__pyx_n_s__k; static PyObject *__pyx_n_s__key; static PyObject *__pyx_n_s__keys; +static PyObject *__pyx_n_s__l; +static PyObject *__pyx_n_s__label; +static PyObject *__pyx_n_s__last; +static PyObject *__pyx_n_s__last_line; +static PyObject *__pyx_n_s__left; static PyObject *__pyx_n_s__leftalign; static PyObject *__pyx_n_s__len; static PyObject *__pyx_n_s__line; static PyObject *__pyx_n_s__lineparse; static PyObject *__pyx_n_s__lines; +static PyObject *__pyx_n_s__longest; static PyObject *__pyx_n_s__map; static PyObject *__pyx_n_s__match; static PyObject *__pyx_n_s__min; static PyObject *__pyx_n_s__missing; static PyObject *__pyx_n_s__missingvalue; +static PyObject *__pyx_n_s__movable; +static PyObject *__pyx_n_s__n; +static PyObject *__pyx_n_s__na; static PyObject *__pyx_n_s__namedtuple; -static PyObject *__pyx_n_s__nfields; +static PyObject *__pyx_n_s__newalts; +static PyObject *__pyx_n_s__nmb; static PyObject *__pyx_n_s__number; static PyObject *__pyx_n_s__numbertype; static PyObject *__pyx_n_s__object; -static PyObject *__pyx_n_s__offset; static PyObject *__pyx_n_s__operator; static PyObject *__pyx_n_s__opt; +static PyObject *__pyx_n_s__output; static PyObject *__pyx_n_s__parse; static PyObject *__pyx_n_s__parse_data; static PyObject *__pyx_n_s__parse_format; @@ -1554,6 +2102,7 @@ static PyObject *__pyx_n_s__pos1; static PyObject *__pyx_n_s__pos2; static PyObject *__pyx_n_s__pysam; static PyObject *__pyx_n_s__qual; +static PyObject *__pyx_n_s__r; static PyObject *__pyx_n_s__range; static PyObject *__pyx_n_s__re; static PyObject *__pyx_n_s__record; @@ -1564,9 +2113,16 @@ static PyObject *__pyx_n_s__reference; static PyObject *__pyx_n_s__region; static PyObject *__pyx_n_s__regions; static PyObject *__pyx_n_s__replace; +static PyObject *__pyx_n_s__required; +static PyObject *__pyx_n_s__rest; +static PyObject *__pyx_n_s__result; +static PyObject *__pyx_n_s__s; +static PyObject *__pyx_n_s__sample; static PyObject *__pyx_n_s__samples; +static PyObject *__pyx_n_s__sdata; static PyObject *__pyx_n_s__self; static PyObject *__pyx_n_s__separator; +static PyObject *__pyx_n_s__sequence; static PyObject *__pyx_n_s__setfilter; static PyObject *__pyx_n_s__setformat; static PyObject *__pyx_n_s__setheader; @@ -1575,18 +2131,23 @@ static PyObject *__pyx_n_s__setreference; static PyObject *__pyx_n_s__setregions; static PyObject *__pyx_n_s__setsamples; static PyObject *__pyx_n_s__setversion; +static PyObject *__pyx_n_s__shortest; static PyObject *__pyx_n_s__split; static PyObject *__pyx_n_s__start; static PyObject *__pyx_n_s__startswith; -static PyObject *__pyx_n_s__stderr; static PyObject *__pyx_n_s__stream; +static PyObject *__pyx_n_s__string; static PyObject *__pyx_n_s__strip; static PyObject *__pyx_n_s__sys; +static PyObject *__pyx_n_s__t; static PyObject *__pyx_n_s__tabixfile; static PyObject *__pyx_n_s__type; static PyObject *__pyx_n_s__upper; +static PyObject *__pyx_n_s__v; static PyObject *__pyx_n_s__validate; static PyObject *__pyx_n_s__value; +static PyObject *__pyx_n_s__values; +static PyObject *__pyx_n_s__var; static PyObject *__pyx_n_s__vcf; static PyObject *__pyx_n_s__vcffile; static PyObject *__pyx_n_s__version; @@ -1596,6 +2157,8 @@ static PyObject *__pyx_n_s__write_data; static PyObject *__pyx_n_s__write_header; static PyObject *__pyx_n_s__write_heading; static PyObject *__pyx_n_s__writeheader; +static PyObject *__pyx_n_s__x; +static PyObject *__pyx_n_s__y; static PyObject *__pyx_n_s__zip; static PyObject *__pyx_int_0; static PyObject *__pyx_int_1; @@ -1629,16 +2192,12 @@ static PyObject *__pyx_int_27; static PyObject *__pyx_int_28; static PyObject *__pyx_int_29; static PyObject *__pyx_int_30; +static PyObject *__pyx_int_31; +static PyObject *__pyx_int_32; static PyObject *__pyx_int_33; static PyObject *__pyx_int_40; static PyObject *__pyx_int_100; static PyObject *__pyx_int_3000000000; -static PyObject *__pyx_k_22; -static PyObject *__pyx_k_26; -static PyObject *__pyx_k_60; -static PyObject *__pyx_k_64; -static PyObject *__pyx_k_65; -static PyObject *__pyx_k_99; static PyObject *__pyx_k_tuple_3; static PyObject *__pyx_k_tuple_5; static PyObject *__pyx_k_tuple_7; @@ -1648,140 +2207,246 @@ static PyObject *__pyx_k_tuple_13; static PyObject *__pyx_k_tuple_15; static PyObject *__pyx_k_tuple_16; static PyObject *__pyx_k_tuple_17; +static PyObject *__pyx_k_tuple_22; static PyObject *__pyx_k_tuple_23; -static PyObject *__pyx_k_tuple_24; -static PyObject *__pyx_k_tuple_28; +static PyObject *__pyx_k_tuple_26; +static PyObject *__pyx_k_tuple_29; +static PyObject *__pyx_k_tuple_30; static PyObject *__pyx_k_tuple_31; -static PyObject *__pyx_k_tuple_32; static PyObject *__pyx_k_tuple_33; +static PyObject *__pyx_k_tuple_34; static PyObject *__pyx_k_tuple_35; -static PyObject *__pyx_k_tuple_36; -static PyObject *__pyx_k_tuple_37; +static PyObject *__pyx_k_tuple_42; +static PyObject *__pyx_k_tuple_43; static PyObject *__pyx_k_tuple_44; static PyObject *__pyx_k_tuple_45; static PyObject *__pyx_k_tuple_46; static PyObject *__pyx_k_tuple_47; static PyObject *__pyx_k_tuple_48; static PyObject *__pyx_k_tuple_49; -static PyObject *__pyx_k_tuple_50; static PyObject *__pyx_k_tuple_51; -static PyObject *__pyx_k_tuple_53; -static PyObject *__pyx_k_tuple_54; -static PyObject *__pyx_k_tuple_67; -static PyObject *__pyx_k_tuple_68; -static PyObject *__pyx_k_tuple_74; -static PyObject *__pyx_k_tuple_75; -static PyObject *__pyx_k_tuple_83; -static PyObject *__pyx_k_tuple_84; +static PyObject *__pyx_k_tuple_52; +static PyObject *__pyx_k_tuple_62; +static PyObject *__pyx_k_tuple_63; +static PyObject *__pyx_k_tuple_77; +static PyObject *__pyx_k_tuple_78; static PyObject *__pyx_k_tuple_86; -static PyObject *__pyx_k_tuple_94; -static PyObject *__pyx_k_tuple_95; -static PyObject *__pyx_k_tuple_96; -static PyObject *__pyx_k_tuple_100; -static PyObject *__pyx_k_tuple_104; -static PyObject *__pyx_k_tuple_105; -static PyObject *__pyx_k_tuple_106; +static PyObject *__pyx_k_tuple_87; +static PyObject *__pyx_k_tuple_89; +static PyObject *__pyx_k_tuple_97; +static PyObject *__pyx_k_tuple_98; +static PyObject *__pyx_k_tuple_99; +static PyObject *__pyx_k_tuple_103; static PyObject *__pyx_k_tuple_107; static PyObject *__pyx_k_tuple_108; static PyObject *__pyx_k_tuple_109; static PyObject *__pyx_k_tuple_110; -static PyObject *__pyx_k_tuple_114; -static PyObject *__pyx_k_tuple_116; +static PyObject *__pyx_k_tuple_111; +static PyObject *__pyx_k_tuple_112; +static PyObject *__pyx_k_tuple_113; static PyObject *__pyx_k_tuple_117; +static PyObject *__pyx_k_tuple_119; static PyObject *__pyx_k_tuple_120; -static PyObject *__pyx_k_tuple_123; +static PyObject *__pyx_k_tuple_122; static PyObject *__pyx_k_tuple_124; -static PyObject *__pyx_k_tuple_125; static PyObject *__pyx_k_tuple_127; static PyObject *__pyx_k_tuple_129; static PyObject *__pyx_k_tuple_131; - -/* "cvcf.pyx":58 - * - * # Utility function. Uses 0-based coordinates - * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<< - * # obtain sequence from .fa file, without truncation - * if end<=start: return "" - */ - -static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pf_4cvcf_get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_k_tuple_132; +static PyObject *__pyx_k_tuple_135; +static PyObject *__pyx_k_tuple_138; +static PyObject *__pyx_k_tuple_173; +static PyObject *__pyx_k_tuple_175; +static PyObject *__pyx_k_tuple_177; +static PyObject *__pyx_k_tuple_178; +static PyObject *__pyx_k_tuple_180; +static PyObject *__pyx_k_tuple_182; +static PyObject *__pyx_k_tuple_184; +static PyObject *__pyx_k_tuple_186; +static PyObject *__pyx_k_tuple_188; +static PyObject *__pyx_k_tuple_190; +static PyObject *__pyx_k_tuple_192; +static PyObject *__pyx_k_tuple_194; +static PyObject *__pyx_k_tuple_196; +static PyObject *__pyx_k_tuple_198; +static PyObject *__pyx_k_tuple_200; +static PyObject *__pyx_k_tuple_202; +static PyObject *__pyx_k_tuple_204; +static PyObject *__pyx_k_tuple_206; +static PyObject *__pyx_k_tuple_208; +static PyObject *__pyx_k_tuple_210; +static PyObject *__pyx_k_tuple_212; +static PyObject *__pyx_k_tuple_214; +static PyObject *__pyx_k_tuple_216; +static PyObject *__pyx_k_tuple_218; +static PyObject *__pyx_k_tuple_220; +static PyObject *__pyx_k_tuple_222; +static PyObject *__pyx_k_tuple_224; +static PyObject *__pyx_k_tuple_226; +static PyObject *__pyx_k_tuple_228; +static PyObject *__pyx_k_tuple_230; +static PyObject *__pyx_k_tuple_232; +static PyObject *__pyx_k_tuple_234; +static PyObject *__pyx_k_tuple_236; +static PyObject *__pyx_k_tuple_238; +static PyObject *__pyx_k_tuple_240; +static PyObject *__pyx_k_tuple_242; +static PyObject *__pyx_k_tuple_244; +static PyObject *__pyx_k_tuple_246; +static PyObject *__pyx_k_tuple_248; +static PyObject *__pyx_k_tuple_250; +static PyObject *__pyx_k_tuple_252; +static PyObject *__pyx_k_tuple_254; +static PyObject *__pyx_k_tuple_256; +static PyObject *__pyx_k_tuple_257; +static PyObject *__pyx_k_codeobj_133; +static PyObject *__pyx_k_codeobj_136; +static PyObject *__pyx_k_codeobj_174; +static PyObject *__pyx_k_codeobj_176; +static PyObject *__pyx_k_codeobj_179; +static PyObject *__pyx_k_codeobj_181; +static PyObject *__pyx_k_codeobj_183; +static PyObject *__pyx_k_codeobj_185; +static PyObject *__pyx_k_codeobj_187; +static PyObject *__pyx_k_codeobj_189; +static PyObject *__pyx_k_codeobj_191; +static PyObject *__pyx_k_codeobj_193; +static PyObject *__pyx_k_codeobj_195; +static PyObject *__pyx_k_codeobj_197; +static PyObject *__pyx_k_codeobj_199; +static PyObject *__pyx_k_codeobj_201; +static PyObject *__pyx_k_codeobj_203; +static PyObject *__pyx_k_codeobj_205; +static PyObject *__pyx_k_codeobj_207; 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+ { PyObject* values[4] = {0,0,0,0}; - switch (PyTuple_GET_SIZE(__pyx_args)) { - case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); - case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); - case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); - case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); - case 0: break; - default: goto __pyx_L5_argtuple_error; - } - switch (PyTuple_GET_SIZE(__pyx_args)) { - case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom); - if (likely(values[0])) kw_args--; - else goto __pyx_L5_argtuple_error; - case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); - if (likely(values[1])) kw_args--; - else { - __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; } - case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); - if (likely(values[2])) kw_args--; - else { - __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom); + if (likely(values[0])) kw_args--; + else goto __pyx_L5_argtuple_error; + case 1: + values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); + if (likely(values[1])) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + case 2: + values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); + if (likely(values[2])) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + case 3: + values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa); + if (likely(values[3])) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } } - case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa); - if (likely(values[3])) kw_args--; - else { - __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_sequence") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } - } - if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "get_sequence") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else if (PyTuple_GET_SIZE(__pyx_args) != 4) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + values[3] = PyTuple_GET_ITEM(__pyx_args, 3); } __pyx_v_chrom = values[0]; __pyx_v_start = values[1]; __pyx_v_end = values[2]; __pyx_v_fa = values[3]; - } else if (PyTuple_GET_SIZE(__pyx_args) != 4) { - goto __pyx_L5_argtuple_error; - } else { - __pyx_v_chrom = PyTuple_GET_ITEM(__pyx_args, 0); - __pyx_v_start = PyTuple_GET_ITEM(__pyx_args, 1); - __pyx_v_end = PyTuple_GET_ITEM(__pyx_args, 2); - __pyx_v_fa = PyTuple_GET_ITEM(__pyx_args, 3); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; 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__pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_t_4(__pyx_t_1); + if (unlikely(!__pyx_t_2)) { + if (PyErr_Occurred()) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); + else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } break; } - __Pyx_GOTREF(__pyx_t_3); + __Pyx_GOTREF(__pyx_t_2); } - __Pyx_DECREF(__pyx_v_r); - __pyx_v_r = __pyx_t_3; - __pyx_t_3 = 0; + __Pyx_XDECREF(__pyx_v_r); + __pyx_v_r = __pyx_t_2; + __pyx_t_2 = 0; /* "cvcf.pyx":71 * result = [] @@ -2081,14 +2760,14 @@ static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *_ * chrom, start, end = elts[0], 0, 3000000000 * if len(elts)==1: pass */ - __pyx_t_3 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__split); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_5), NULL); 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goto __pyx_L1_error;} - __pyx_t_7 = (__pyx_t_6 == 2); - if (__pyx_t_7) { + __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = (__pyx_t_7 == 2); + if (__pyx_t_8) { /* "cvcf.pyx":75 * if len(elts)==1: pass @@ -2144,12 +2823,12 @@ static PyObject *__pyx_pf_4cvcf_1parse_regions(PyObject *__pyx_self, PyObject *_ * ielts = elts[1].split('-') * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) */ - __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = (__pyx_t_6 > 0); 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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Flag)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_63)); - PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_60)); + PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_60)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); 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goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -7679,21 +9034,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_INCREF(((PyObject *)__pyx_n_s__Float)); PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__Float)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Float)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_63)); - PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_60)); + PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_60)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60)); __Pyx_INCREF(Py_None); PyTuple_SET_ITEM(__pyx_t_2, 5, Py_None); __Pyx_GIVEREF(Py_None); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setformat") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_self = values[0]; __pyx_v_format = values[1]; - } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { - goto __pyx_L5_argtuple_error; - } else { - __pyx_v_self = PyTuple_GET_ITEM(__pyx_args, 0); - __pyx_v_format = PyTuple_GET_ITEM(__pyx_args, 1); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; 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goto __pyx_L3_error;} + } } - case 6: - values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2); - if (likely(values[6])) kw_args--; - else { - __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compare_calls") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } - } - if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "compare_calls") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } else if (PyTuple_GET_SIZE(__pyx_args) != 7) { + goto __pyx_L5_argtuple_error; + } else { + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); 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__pyx_tp_dealloc_4cvcf_asVCFRecord, /*tp_dealloc*/ - 0, /*tp_print*/ - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ - #if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ - #else - 0, /*reserved*/ - #endif - 0, /*tp_repr*/ - &__pyx_tp_as_number_asVCFRecord, /*tp_as_number*/ - &__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/ - 0, /*tp_hash*/ - __pyx_pf_4cvcf_11asVCFRecord_1__call__, /*tp_call*/ - 0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_asVCFRecord, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/ - __pyx_tp_traverse_4cvcf_asVCFRecord, /*tp_traverse*/ - __pyx_tp_clear_4cvcf_asVCFRecord, /*tp_clear*/ - 0, /*tp_richcompare*/ - 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_4cvcf_asVCFRecord, /*tp_methods*/ - 0, /*tp_members*/ - 0, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - 0, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - 0, /*tp_dictoffset*/ - __pyx_pf_4cvcf_11asVCFRecord___init__, /*tp_init*/ - 0, /*tp_alloc*/ - __pyx_tp_new_4cvcf_asVCFRecord, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - 0, /*tp_del*/ - #if PY_VERSION_HEX >= 0x02060000 - 0, /*tp_version_tag*/ - #endif -}; - -static PyMethodDef __pyx_methods[] = { - {0, 0, 0, 0} -}; - -#if PY_MAJOR_VERSION >= 3 -static struct PyModuleDef __pyx_moduledef = { - PyModuleDef_HEAD_INIT, - __Pyx_NAMESTR("cvcf"), - 0, /* m_doc */ - -1, /* m_size */ - __pyx_methods /* m_methods */, - NULL, /* m_reload */ - NULL, /* m_traverse */ - NULL, /* m_clear */ - NULL /* m_free */ -}; -#endif +#if PY_MAJOR_VERSION >= 3 +static struct PyModuleDef __pyx_moduledef = { + PyModuleDef_HEAD_INIT, + __Pyx_NAMESTR("cvcf"), + 0, /* m_doc */ + -1, /* m_size */ + __pyx_methods /* m_methods */, + NULL, /* m_reload */ + NULL, /* m_traverse */ + NULL, /* m_clear */ + NULL /* m_free */ +}; +#endif static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 1, 0}, + {&__pyx_n_s_100, __pyx_k_100, sizeof(__pyx_k_100), 0, 0, 1, 1}, {&__pyx_n_s_101, __pyx_k_101, sizeof(__pyx_k_101), 0, 0, 1, 1}, - 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{&__pyx_kp_s_63, __pyx_k_63, sizeof(__pyx_k_63), 0, 0, 1, 0}, + {&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0}, + {&__pyx_kp_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 0}, {&__pyx_kp_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 0}, + {&__pyx_kp_s_67, __pyx_k_67, sizeof(__pyx_k_67), 0, 0, 1, 0}, + {&__pyx_kp_s_68, __pyx_k_68, sizeof(__pyx_k_68), 0, 0, 1, 0}, {&__pyx_kp_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 0}, {&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0}, {&__pyx_kp_s_71, __pyx_k_71, sizeof(__pyx_k_71), 0, 0, 1, 0}, {&__pyx_kp_s_72, __pyx_k_72, sizeof(__pyx_k_72), 0, 0, 1, 0}, {&__pyx_kp_s_73, __pyx_k_73, sizeof(__pyx_k_73), 0, 0, 1, 0}, + {&__pyx_kp_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 0}, + {&__pyx_kp_s_75, __pyx_k_75, sizeof(__pyx_k_75), 0, 0, 1, 0}, {&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0}, - {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0}, - {&__pyx_kp_s_78, __pyx_k_78, sizeof(__pyx_k_78), 0, 0, 1, 0}, - {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1}, + {&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0}, {&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0}, {&__pyx_kp_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 0}, {&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0}, - {&__pyx_kp_s_82, __pyx_k_82, sizeof(__pyx_k_82), 0, 0, 1, 0}, + {&__pyx_n_s_82, __pyx_k_82, sizeof(__pyx_k_82), 0, 0, 1, 1}, + {&__pyx_kp_s_83, __pyx_k_83, sizeof(__pyx_k_83), 0, 0, 1, 0}, + {&__pyx_kp_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 0}, {&__pyx_kp_s_85, __pyx_k_85, sizeof(__pyx_k_85), 0, 0, 1, 0}, - {&__pyx_n_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 1}, {&__pyx_kp_s_88, __pyx_k_88, sizeof(__pyx_k_88), 0, 0, 1, 0}, - {&__pyx_kp_s_89, __pyx_k_89, sizeof(__pyx_k_89), 0, 0, 1, 0}, {&__pyx_kp_b_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 0, 0}, {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0}, {&__pyx_n_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 1}, {&__pyx_kp_s_91, __pyx_k_91, sizeof(__pyx_k_91), 0, 0, 1, 0}, {&__pyx_kp_s_92, __pyx_k_92, sizeof(__pyx_k_92), 0, 0, 1, 0}, {&__pyx_n_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 1}, - {&__pyx_n_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 1}, - {&__pyx_n_s_98, __pyx_k_98, sizeof(__pyx_k_98), 0, 0, 1, 1}, + {&__pyx_kp_s_94, __pyx_k_94, sizeof(__pyx_k_94), 0, 0, 1, 0}, + {&__pyx_kp_s_95, __pyx_k_95, sizeof(__pyx_k_95), 0, 0, 1, 0}, + {&__pyx_n_s_96, __pyx_k_96, sizeof(__pyx_k_96), 0, 0, 1, 1}, {&__pyx_kp_b__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 0, 0}, {&__pyx_kp_s__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 1, 0}, + {&__pyx_n_s__A, __pyx_k__A, sizeof(__pyx_k__A), 0, 0, 1, 1}, {&__pyx_n_s__ACGTN, __pyx_k__ACGTN, sizeof(__pyx_k__ACGTN), 0, 0, 1, 1}, {&__pyx_n_s__ALT, __pyx_k__ALT, sizeof(__pyx_k__ALT), 0, 0, 1, 1}, {&__pyx_n_s__BAD_GENOTYPE, __pyx_k__BAD_GENOTYPE, sizeof(__pyx_k__BAD_GENOTYPE), 0, 0, 1, 1}, @@ -23108,6 +24108,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__D, __pyx_k__D, sizeof(__pyx_k__D), 0, 0, 1, 1}, {&__pyx_n_s__DP, __pyx_k__DP, sizeof(__pyx_k__DP), 0, 0, 1, 1}, {&__pyx_n_s__Description, __pyx_k__Description, sizeof(__pyx_k__Description), 0, 0, 1, 1}, + {&__pyx_n_s__EC, __pyx_k__EC, sizeof(__pyx_k__EC), 0, 0, 1, 1}, {&__pyx_n_s__ERROR_INFO_STRING, __pyx_k__ERROR_INFO_STRING, sizeof(__pyx_k__ERROR_INFO_STRING), 0, 0, 1, 1}, {&__pyx_n_s__ERROR_TRAILING_DATA, __pyx_k__ERROR_TRAILING_DATA, sizeof(__pyx_k__ERROR_TRAILING_DATA), 0, 0, 1, 1}, {&__pyx_n_s__ERROR_UNKNOWN_KEY, __pyx_k__ERROR_UNKNOWN_KEY, sizeof(__pyx_k__ERROR_UNKNOWN_KEY), 0, 0, 1, 1}, @@ -23119,6 +24120,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__FT, __pyx_k__FT, sizeof(__pyx_k__FT), 0, 0, 1, 1}, {&__pyx_n_s__Flag, __pyx_k__Flag, sizeof(__pyx_k__Flag), 0, 0, 1, 1}, {&__pyx_n_s__Float, __pyx_k__Float, sizeof(__pyx_k__Float), 0, 0, 1, 1}, + {&__pyx_n_s__G, __pyx_k__G, sizeof(__pyx_k__G), 0, 0, 1, 1}, + {&__pyx_n_s__GL, __pyx_k__GL, sizeof(__pyx_k__GL), 0, 0, 1, 1}, + {&__pyx_n_s__GLE, __pyx_k__GLE, sizeof(__pyx_k__GLE), 0, 0, 1, 1}, + {&__pyx_n_s__GP, __pyx_k__GP, sizeof(__pyx_k__GP), 0, 0, 1, 1}, {&__pyx_n_s__GQ, __pyx_k__GQ, sizeof(__pyx_k__GQ), 0, 0, 1, 1}, {&__pyx_n_s__GT, __pyx_k__GT, sizeof(__pyx_k__GT), 0, 0, 1, 1}, {&__pyx_n_s__GTdata, __pyx_k__GTdata, sizeof(__pyx_k__GTdata), 0, 0, 1, 1}, @@ -23131,6 +24136,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__Integer, __pyx_k__Integer, sizeof(__pyx_k__Integer), 0, 0, 1, 1}, {&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1}, {&__pyx_n_s__MISSING_REF, __pyx_k__MISSING_REF, sizeof(__pyx_k__MISSING_REF), 0, 0, 1, 1}, + {&__pyx_n_s__MQ, __pyx_k__MQ, sizeof(__pyx_k__MQ), 0, 0, 1, 1}, {&__pyx_n_s__N, __pyx_k__N, sizeof(__pyx_k__N), 0, 0, 1, 1}, {&__pyx_n_s__NT_ALLELES, __pyx_k__NT_ALLELES, sizeof(__pyx_k__NT_ALLELES), 0, 0, 1, 1}, {&__pyx_n_s__NT_GENOTYPES, __pyx_k__NT_GENOTYPES, sizeof(__pyx_k__NT_GENOTYPES), 0, 0, 1, 1}, @@ -23142,9 +24148,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__Number, __pyx_k__Number, sizeof(__pyx_k__Number), 0, 0, 1, 1}, {&__pyx_n_b__PASS, __pyx_k__PASS, sizeof(__pyx_k__PASS), 0, 0, 0, 1}, {&__pyx_n_s__PASS, __pyx_k__PASS, sizeof(__pyx_k__PASS), 0, 0, 1, 1}, + {&__pyx_n_s__PL, __pyx_k__PL, sizeof(__pyx_k__PL), 0, 0, 1, 1}, {&__pyx_n_s__POS, __pyx_k__POS, sizeof(__pyx_k__POS), 0, 0, 1, 1}, {&__pyx_n_s__POS_NOT_NUMERICAL, __pyx_k__POS_NOT_NUMERICAL, sizeof(__pyx_k__POS_NOT_NUMERICAL), 0, 0, 1, 1}, {&__pyx_n_s__POS_NOT_POSITIVE, __pyx_k__POS_NOT_POSITIVE, sizeof(__pyx_k__POS_NOT_POSITIVE), 0, 0, 1, 1}, + {&__pyx_n_s__PQ, __pyx_k__PQ, sizeof(__pyx_k__PQ), 0, 0, 1, 1}, + {&__pyx_n_s__PS, __pyx_k__PS, sizeof(__pyx_k__PS), 0, 0, 1, 1}, {&__pyx_n_s__QUAL, __pyx_k__QUAL, sizeof(__pyx_k__QUAL), 0, 0, 1, 1}, {&__pyx_n_s__QUAL_NOT_NUMERICAL, __pyx_k__QUAL_NOT_NUMERICAL, sizeof(__pyx_k__QUAL_NOT_NUMERICAL), 0, 0, 1, 1}, {&__pyx_n_s__REF, __pyx_k__REF, sizeof(__pyx_k__REF), 0, 0, 1, 1}, @@ -23188,47 +24197,63 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s___samples, __pyx_k___samples, sizeof(__pyx_k___samples), 0, 0, 1, 1}, {&__pyx_n_s___version, __pyx_k___version, sizeof(__pyx_k___version), 0, 0, 1, 1}, {&__pyx_n_s___warn_errors, __pyx_k___warn_errors, sizeof(__pyx_k___warn_errors), 0, 0, 1, 1}, + {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1}, {&__pyx_n_s__add, __pyx_k__add, sizeof(__pyx_k__add), 0, 0, 1, 1}, + {&__pyx_n_s__addn, __pyx_k__addn, sizeof(__pyx_k__addn), 0, 0, 1, 1}, + {&__pyx_n_s__addns, __pyx_k__addns, sizeof(__pyx_k__addns), 0, 0, 1, 1}, + {&__pyx_n_s__allele, __pyx_k__allele, sizeof(__pyx_k__allele), 0, 0, 1, 1}, {&__pyx_n_s__alleleRegEx, __pyx_k__alleleRegEx, sizeof(__pyx_k__alleleRegEx), 0, 0, 1, 1}, {&__pyx_n_s__alt, __pyx_k__alt, sizeof(__pyx_k__alt), 0, 0, 1, 1}, {&__pyx_n_s__alt1, __pyx_k__alt1, sizeof(__pyx_k__alt1), 0, 0, 1, 1}, {&__pyx_n_s__alt2, __pyx_k__alt2, sizeof(__pyx_k__alt2), 0, 0, 1, 1}, - {&__pyx_n_s__append, __pyx_k__append, sizeof(__pyx_k__append), 0, 0, 1, 1}, {&__pyx_n_s__bisect, __pyx_k__bisect, sizeof(__pyx_k__bisect), 0, 0, 1, 1}, + {&__pyx_n_s__blurp, __pyx_k__blurp, sizeof(__pyx_k__blurp), 0, 0, 1, 1}, {&__pyx_n_s__buffer, __pyx_k__buffer, sizeof(__pyx_k__buffer), 0, 0, 1, 1}, + {&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1}, {&__pyx_n_s__chrom, __pyx_k__chrom, sizeof(__pyx_k__chrom), 0, 0, 1, 1}, {&__pyx_n_s__collections, __pyx_k__collections, sizeof(__pyx_k__collections), 0, 0, 1, 1}, + {&__pyx_n_s__cols, __pyx_k__cols, sizeof(__pyx_k__cols), 0, 0, 1, 1}, {&__pyx_n_s__compare_calls, __pyx_k__compare_calls, sizeof(__pyx_k__compare_calls), 0, 0, 1, 1}, {&__pyx_n_s__compile, __pyx_k__compile, sizeof(__pyx_k__compile), 0, 0, 1, 1}, {&__pyx_n_s__connect, __pyx_k__connect, sizeof(__pyx_k__connect), 0, 0, 1, 1}, - {&__pyx_n_s__contig, __pyx_k__contig, sizeof(__pyx_k__contig), 0, 0, 1, 1}, {&__pyx_n_s__convertGT, __pyx_k__convertGT, sizeof(__pyx_k__convertGT), 0, 0, 1, 1}, {&__pyx_n_s__convertGTback, __pyx_k__convertGTback, sizeof(__pyx_k__convertGTback), 0, 0, 1, 1}, {&__pyx_n_s__copy, __pyx_k__copy, sizeof(__pyx_k__copy), 0, 0, 1, 1}, {&__pyx_n_s__cvcf, __pyx_k__cvcf, sizeof(__pyx_k__cvcf), 0, 0, 1, 1}, + {&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1}, {&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1}, {&__pyx_n_s__datagenerator, __pyx_k__datagenerator, sizeof(__pyx_k__datagenerator), 0, 0, 1, 1}, {&__pyx_n_s__deepcopy, __pyx_k__deepcopy, sizeof(__pyx_k__deepcopy), 0, 0, 1, 1}, {&__pyx_n_s__defaultdict, __pyx_k__defaultdict, sizeof(__pyx_k__defaultdict), 0, 0, 1, 1}, {&__pyx_n_s__descr, __pyx_k__descr, sizeof(__pyx_k__descr), 0, 0, 1, 1}, {&__pyx_n_s__description, __pyx_k__description, sizeof(__pyx_k__description), 0, 0, 1, 1}, + {&__pyx_n_s__dict, __pyx_k__dict, sizeof(__pyx_k__dict), 0, 0, 1, 1}, + {&__pyx_n_s__elts, __pyx_k__elts, sizeof(__pyx_k__elts), 0, 0, 1, 1}, {&__pyx_n_s__end, __pyx_k__end, sizeof(__pyx_k__end), 0, 0, 1, 1}, {&__pyx_n_s__endswith, __pyx_k__endswith, sizeof(__pyx_k__endswith), 0, 0, 1, 1}, {&__pyx_n_s__enumerate, __pyx_k__enumerate, sizeof(__pyx_k__enumerate), 0, 0, 1, 1}, + {&__pyx_n_s__err, __pyx_k__err, sizeof(__pyx_k__err), 0, 0, 1, 1}, {&__pyx_n_s__error, __pyx_k__error, sizeof(__pyx_k__error), 0, 0, 1, 1}, + {&__pyx_n_s__errorlabel, __pyx_k__errorlabel, sizeof(__pyx_k__errorlabel), 0, 0, 1, 1}, {&__pyx_n_s__errorstring, __pyx_k__errorstring, sizeof(__pyx_k__errorstring), 0, 0, 1, 1}, + {&__pyx_n_s__errwarn, __pyx_k__errwarn, sizeof(__pyx_k__errwarn), 0, 0, 1, 1}, + {&__pyx_n_s__expected, __pyx_k__expected, sizeof(__pyx_k__expected), 0, 0, 1, 1}, + {&__pyx_n_s__f, __pyx_k__f, sizeof(__pyx_k__f), 0, 0, 1, 1}, {&__pyx_n_s__fa, __pyx_k__fa, sizeof(__pyx_k__fa), 0, 0, 1, 1}, + {&__pyx_n_s__faref, __pyx_k__faref, sizeof(__pyx_k__faref), 0, 0, 1, 1}, + {&__pyx_n_s__faref_leftflank, __pyx_k__faref_leftflank, sizeof(__pyx_k__faref_leftflank), 0, 0, 1, 1}, {&__pyx_n_s__fetch, __pyx_k__fetch, sizeof(__pyx_k__fetch), 0, 0, 1, 1}, - {&__pyx_n_s__fields, __pyx_k__fields, sizeof(__pyx_k__fields), 0, 0, 1, 1}, {&__pyx_n_s__fileformat, __pyx_k__fileformat, sizeof(__pyx_k__fileformat), 0, 0, 1, 1}, {&__pyx_n_s__filename, __pyx_k__filename, sizeof(__pyx_k__filename), 0, 0, 1, 1}, {&__pyx_n_s__filter, __pyx_k__filter, sizeof(__pyx_k__filter), 0, 0, 1, 1}, {&__pyx_n_s__find, __pyx_k__find, sizeof(__pyx_k__find), 0, 0, 1, 1}, + {&__pyx_n_s__first, __pyx_k__first, sizeof(__pyx_k__first), 0, 0, 1, 1}, {&__pyx_n_s__fmt, __pyx_k__fmt, sizeof(__pyx_k__fmt), 0, 0, 1, 1}, {&__pyx_n_s__format, __pyx_k__format, sizeof(__pyx_k__format), 0, 0, 1, 1}, {&__pyx_n_s__format_format, __pyx_k__format_format, sizeof(__pyx_k__format_format), 0, 0, 1, 1}, {&__pyx_n_s__format_formatdata, __pyx_k__format_formatdata, sizeof(__pyx_k__format_formatdata), 0, 0, 1, 1}, {&__pyx_n_s__formatdict, __pyx_k__formatdict, sizeof(__pyx_k__formatdict), 0, 0, 1, 1}, + {&__pyx_n_s__genexpr, __pyx_k__genexpr, sizeof(__pyx_k__genexpr), 0, 0, 1, 1}, {&__pyx_n_s__get, __pyx_k__get, sizeof(__pyx_k__get), 0, 0, 1, 1}, {&__pyx_n_s__get_expected, __pyx_k__get_expected, sizeof(__pyx_k__get_expected), 0, 0, 1, 1}, {&__pyx_n_s__get_sequence, __pyx_k__get_sequence, sizeof(__pyx_k__get_sequence), 0, 0, 1, 1}, @@ -23237,35 +24262,52 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__getheader, __pyx_k__getheader, sizeof(__pyx_k__getheader), 0, 0, 1, 1}, {&__pyx_n_s__getinfo, __pyx_k__getinfo, sizeof(__pyx_k__getinfo), 0, 0, 1, 1}, {&__pyx_n_s__getsamples, __pyx_k__getsamples, sizeof(__pyx_k__getsamples), 0, 0, 1, 1}, + {&__pyx_n_s__gts, __pyx_k__gts, sizeof(__pyx_k__gts), 0, 0, 1, 1}, {&__pyx_n_s__gtsRegEx, __pyx_k__gtsRegEx, sizeof(__pyx_k__gtsRegEx), 0, 0, 1, 1}, + {&__pyx_n_s__have_deletions, __pyx_k__have_deletions, sizeof(__pyx_k__have_deletions), 0, 0, 1, 1}, {&__pyx_n_s__header, __pyx_k__header, sizeof(__pyx_k__header), 0, 0, 1, 1}, + {&__pyx_n_s__headings, __pyx_k__headings, sizeof(__pyx_k__headings), 0, 0, 1, 1}, + {&__pyx_n_s__i, __pyx_k__i, sizeof(__pyx_k__i), 0, 0, 1, 1}, {&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1}, + {&__pyx_n_s__idx, __pyx_k__idx, sizeof(__pyx_k__idx), 0, 0, 1, 1}, + {&__pyx_n_s__ielts, __pyx_k__ielts, sizeof(__pyx_k__ielts), 0, 0, 1, 1}, {&__pyx_n_s__ignoreerror, __pyx_k__ignoreerror, sizeof(__pyx_k__ignoreerror), 0, 0, 1, 1}, {&__pyx_n_s__info, __pyx_k__info, sizeof(__pyx_k__info), 0, 0, 1, 1}, {&__pyx_n_s__inregion, __pyx_k__inregion, sizeof(__pyx_k__inregion), 0, 0, 1, 1}, {&__pyx_n_s__itemgetter, __pyx_k__itemgetter, sizeof(__pyx_k__itemgetter), 0, 0, 1, 1}, {&__pyx_n_s__itervalues, __pyx_k__itervalues, sizeof(__pyx_k__itervalues), 0, 0, 1, 1}, {&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1}, + {&__pyx_n_s__k, __pyx_k__k, sizeof(__pyx_k__k), 0, 0, 1, 1}, {&__pyx_n_s__key, __pyx_k__key, sizeof(__pyx_k__key), 0, 0, 1, 1}, {&__pyx_n_s__keys, __pyx_k__keys, sizeof(__pyx_k__keys), 0, 0, 1, 1}, + {&__pyx_n_s__l, __pyx_k__l, sizeof(__pyx_k__l), 0, 0, 1, 1}, + {&__pyx_n_s__label, __pyx_k__label, sizeof(__pyx_k__label), 0, 0, 1, 1}, + {&__pyx_n_s__last, __pyx_k__last, sizeof(__pyx_k__last), 0, 0, 1, 1}, + {&__pyx_n_s__last_line, __pyx_k__last_line, sizeof(__pyx_k__last_line), 0, 0, 1, 1}, + {&__pyx_n_s__left, __pyx_k__left, sizeof(__pyx_k__left), 0, 0, 1, 1}, {&__pyx_n_s__leftalign, __pyx_k__leftalign, sizeof(__pyx_k__leftalign), 0, 0, 1, 1}, {&__pyx_n_s__len, __pyx_k__len, sizeof(__pyx_k__len), 0, 0, 1, 1}, {&__pyx_n_s__line, __pyx_k__line, sizeof(__pyx_k__line), 0, 0, 1, 1}, {&__pyx_n_s__lineparse, __pyx_k__lineparse, sizeof(__pyx_k__lineparse), 0, 0, 1, 1}, {&__pyx_n_s__lines, __pyx_k__lines, sizeof(__pyx_k__lines), 0, 0, 1, 1}, + {&__pyx_n_s__longest, __pyx_k__longest, sizeof(__pyx_k__longest), 0, 0, 1, 1}, {&__pyx_n_s__map, __pyx_k__map, sizeof(__pyx_k__map), 0, 0, 1, 1}, {&__pyx_n_s__match, __pyx_k__match, sizeof(__pyx_k__match), 0, 0, 1, 1}, {&__pyx_n_s__min, __pyx_k__min, sizeof(__pyx_k__min), 0, 0, 1, 1}, {&__pyx_n_s__missing, __pyx_k__missing, sizeof(__pyx_k__missing), 0, 0, 1, 1}, {&__pyx_n_s__missingvalue, __pyx_k__missingvalue, sizeof(__pyx_k__missingvalue), 0, 0, 1, 1}, + {&__pyx_n_s__movable, __pyx_k__movable, sizeof(__pyx_k__movable), 0, 0, 1, 1}, + {&__pyx_n_s__n, __pyx_k__n, sizeof(__pyx_k__n), 0, 0, 1, 1}, + {&__pyx_n_s__na, __pyx_k__na, sizeof(__pyx_k__na), 0, 0, 1, 1}, {&__pyx_n_s__namedtuple, __pyx_k__namedtuple, sizeof(__pyx_k__namedtuple), 0, 0, 1, 1}, - {&__pyx_n_s__nfields, __pyx_k__nfields, sizeof(__pyx_k__nfields), 0, 0, 1, 1}, + {&__pyx_n_s__newalts, __pyx_k__newalts, sizeof(__pyx_k__newalts), 0, 0, 1, 1}, + {&__pyx_n_s__nmb, __pyx_k__nmb, sizeof(__pyx_k__nmb), 0, 0, 1, 1}, {&__pyx_n_s__number, __pyx_k__number, sizeof(__pyx_k__number), 0, 0, 1, 1}, {&__pyx_n_s__numbertype, __pyx_k__numbertype, sizeof(__pyx_k__numbertype), 0, 0, 1, 1}, {&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1}, - {&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1}, {&__pyx_n_s__operator, __pyx_k__operator, sizeof(__pyx_k__operator), 0, 0, 1, 1}, {&__pyx_n_s__opt, __pyx_k__opt, sizeof(__pyx_k__opt), 0, 0, 1, 1}, + {&__pyx_n_s__output, __pyx_k__output, sizeof(__pyx_k__output), 0, 0, 1, 1}, {&__pyx_n_s__parse, __pyx_k__parse, sizeof(__pyx_k__parse), 0, 0, 1, 1}, {&__pyx_n_s__parse_data, __pyx_k__parse_data, sizeof(__pyx_k__parse_data), 0, 0, 1, 1}, {&__pyx_n_s__parse_format, __pyx_k__parse_format, sizeof(__pyx_k__parse_format), 0, 0, 1, 1}, @@ -23279,6 +24321,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__pos2, __pyx_k__pos2, sizeof(__pyx_k__pos2), 0, 0, 1, 1}, {&__pyx_n_s__pysam, __pyx_k__pysam, sizeof(__pyx_k__pysam), 0, 0, 1, 1}, {&__pyx_n_s__qual, __pyx_k__qual, sizeof(__pyx_k__qual), 0, 0, 1, 1}, + {&__pyx_n_s__r, __pyx_k__r, sizeof(__pyx_k__r), 0, 0, 1, 1}, {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1}, {&__pyx_n_s__re, __pyx_k__re, sizeof(__pyx_k__re), 0, 0, 1, 1}, {&__pyx_n_s__record, __pyx_k__record, sizeof(__pyx_k__record), 0, 0, 1, 1}, @@ -23289,9 +24332,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__region, __pyx_k__region, sizeof(__pyx_k__region), 0, 0, 1, 1}, {&__pyx_n_s__regions, __pyx_k__regions, sizeof(__pyx_k__regions), 0, 0, 1, 1}, {&__pyx_n_s__replace, __pyx_k__replace, sizeof(__pyx_k__replace), 0, 0, 1, 1}, + {&__pyx_n_s__required, __pyx_k__required, sizeof(__pyx_k__required), 0, 0, 1, 1}, + {&__pyx_n_s__rest, __pyx_k__rest, sizeof(__pyx_k__rest), 0, 0, 1, 1}, + {&__pyx_n_s__result, __pyx_k__result, sizeof(__pyx_k__result), 0, 0, 1, 1}, + {&__pyx_n_s__s, __pyx_k__s, sizeof(__pyx_k__s), 0, 0, 1, 1}, + {&__pyx_n_s__sample, __pyx_k__sample, sizeof(__pyx_k__sample), 0, 0, 1, 1}, {&__pyx_n_s__samples, __pyx_k__samples, sizeof(__pyx_k__samples), 0, 0, 1, 1}, + {&__pyx_n_s__sdata, __pyx_k__sdata, sizeof(__pyx_k__sdata), 0, 0, 1, 1}, {&__pyx_n_s__self, __pyx_k__self, sizeof(__pyx_k__self), 0, 0, 1, 1}, {&__pyx_n_s__separator, __pyx_k__separator, sizeof(__pyx_k__separator), 0, 0, 1, 1}, + {&__pyx_n_s__sequence, __pyx_k__sequence, sizeof(__pyx_k__sequence), 0, 0, 1, 1}, {&__pyx_n_s__setfilter, __pyx_k__setfilter, sizeof(__pyx_k__setfilter), 0, 0, 1, 1}, {&__pyx_n_s__setformat, __pyx_k__setformat, sizeof(__pyx_k__setformat), 0, 0, 1, 1}, {&__pyx_n_s__setheader, __pyx_k__setheader, sizeof(__pyx_k__setheader), 0, 0, 1, 1}, @@ -23300,18 +24350,23 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__setregions, __pyx_k__setregions, sizeof(__pyx_k__setregions), 0, 0, 1, 1}, {&__pyx_n_s__setsamples, __pyx_k__setsamples, sizeof(__pyx_k__setsamples), 0, 0, 1, 1}, {&__pyx_n_s__setversion, __pyx_k__setversion, sizeof(__pyx_k__setversion), 0, 0, 1, 1}, + {&__pyx_n_s__shortest, __pyx_k__shortest, sizeof(__pyx_k__shortest), 0, 0, 1, 1}, {&__pyx_n_s__split, __pyx_k__split, sizeof(__pyx_k__split), 0, 0, 1, 1}, {&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1}, {&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1}, - {&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1}, {&__pyx_n_s__stream, __pyx_k__stream, sizeof(__pyx_k__stream), 0, 0, 1, 1}, + {&__pyx_n_s__string, __pyx_k__string, sizeof(__pyx_k__string), 0, 0, 1, 1}, {&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1}, {&__pyx_n_s__sys, __pyx_k__sys, sizeof(__pyx_k__sys), 0, 0, 1, 1}, + {&__pyx_n_s__t, __pyx_k__t, sizeof(__pyx_k__t), 0, 0, 1, 1}, {&__pyx_n_s__tabixfile, __pyx_k__tabixfile, sizeof(__pyx_k__tabixfile), 0, 0, 1, 1}, {&__pyx_n_s__type, __pyx_k__type, sizeof(__pyx_k__type), 0, 0, 1, 1}, {&__pyx_n_s__upper, __pyx_k__upper, sizeof(__pyx_k__upper), 0, 0, 1, 1}, + {&__pyx_n_s__v, __pyx_k__v, sizeof(__pyx_k__v), 0, 0, 1, 1}, {&__pyx_n_s__validate, __pyx_k__validate, sizeof(__pyx_k__validate), 0, 0, 1, 1}, {&__pyx_n_s__value, __pyx_k__value, sizeof(__pyx_k__value), 0, 0, 1, 1}, + {&__pyx_n_s__values, __pyx_k__values, sizeof(__pyx_k__values), 0, 0, 1, 1}, + {&__pyx_n_s__var, __pyx_k__var, sizeof(__pyx_k__var), 0, 0, 1, 1}, {&__pyx_n_s__vcf, __pyx_k__vcf, sizeof(__pyx_k__vcf), 0, 0, 1, 1}, {&__pyx_n_s__vcffile, __pyx_k__vcffile, sizeof(__pyx_k__vcffile), 0, 0, 1, 1}, {&__pyx_n_s__version, __pyx_k__version, sizeof(__pyx_k__version), 0, 0, 1, 1}, @@ -23321,765 +24376,1974 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__write_header, __pyx_k__write_header, sizeof(__pyx_k__write_header), 0, 0, 1, 1}, {&__pyx_n_s__write_heading, __pyx_k__write_heading, sizeof(__pyx_k__write_heading), 0, 0, 1, 1}, {&__pyx_n_s__writeheader, __pyx_k__writeheader, sizeof(__pyx_k__writeheader), 0, 0, 1, 1}, + {&__pyx_n_s__x, __pyx_k__x, sizeof(__pyx_k__x), 0, 0, 1, 1}, + {&__pyx_n_s__y, __pyx_k__y, sizeof(__pyx_k__y), 0, 0, 1, 1}, {&__pyx_n_s__zip, __pyx_k__zip, sizeof(__pyx_k__zip), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - 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} - __pyx_refnanny = __Pyx_RefNanny->SetupContext("PyMODINIT_FUNC PyInit_cvcf(void)", __LINE__, __FILE__); #endif + __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_cvcf(void)", 0); + if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - #ifdef __pyx_binding_PyCFunctionType_USED - if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifdef __Pyx_CyFunction_USED + if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_FusedFunction_USED + if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_Generator_USED + if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif /*--- Library function declarations ---*/ /*--- Threads initialization code ---*/ @@ -24190,6 +26460,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) /*--- Constants init code ---*/ if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Global init code ---*/ + /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -24204,19 +26475,37 @@ PyMODINIT_FUNC PyInit_cvcf(void) __pyx_ptype_4cvcf_VCFRecord = &__pyx_type_4cvcf_VCFRecord; __pyx_ptype_6ctabix_Parser = __Pyx_ImportType("ctabix", "Parser", sizeof(struct __pyx_obj_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_4cvcf_asVCFRecord.tp_base = __pyx_ptype_6ctabix_Parser; - if (PyType_Ready(&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_4cvcf_asVCFRecord = &__pyx_type_4cvcf_asVCFRecord; + if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_4cvcf___pyx_scope_struct__parse_data = &__pyx_type_4cvcf___pyx_scope_struct__parse_data; + if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr = &__pyx_type_4cvcf___pyx_scope_struct_1_genexpr; + if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_4cvcf___pyx_scope_struct_2__parse; /*--- Type import code ---*/ __pyx_ptype_6ctabix_Tabixfile = __Pyx_ImportType("ctabix", "Tabixfile", sizeof(struct __pyx_obj_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_TabixIterator = __Pyx_ImportType("ctabix", "TabixIterator", sizeof(struct __pyx_obj_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_TabixHeaderIterator = __Pyx_ImportType("ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_asTuple = __Pyx_ImportType("ctabix", "asTuple", sizeof(struct __pyx_obj_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_asGTF = __Pyx_ImportType("ctabix", "asGTF", sizeof(struct __pyx_obj_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_asBed = __Pyx_ImportType("ctabix", "asBed", sizeof(struct __pyx_obj_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_asVCF = __Pyx_ImportType("ctabix", "asVCF", sizeof(struct __pyx_obj_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_TabixIteratorParsed = __Pyx_ImportType("ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_tabix_inplace_iterator = __Pyx_ImportType("ctabix", "tabix_inplace_iterator", sizeof(struct __pyx_obj_6ctabix_tabix_inplace_iterator), 1); if (unlikely(!__pyx_ptype_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_6ctabix_tabix_inplace_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_inplace_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_6ctabix_tabix_copy_iterator = __Pyx_ImportType("ctabix", "tabix_copy_iterator", sizeof(struct __pyx_obj_6ctabix_tabix_copy_iterator), 1); if (unlikely(!__pyx_ptype_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ @@ -24228,21 +26517,29 @@ PyMODINIT_FUNC PyInit_cvcf(void) * import sys, re, copy, bisect */ __pyx_t_1 = PyList_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_n_s__namedtuple)); PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__namedtuple)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__namedtuple)); __Pyx_INCREF(((PyObject *)__pyx_n_s__defaultdict)); PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__defaultdict)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__defaultdict)); - __pyx_t_2 = __Pyx_Import(((PyObject *)__pyx_n_s__collections), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_Import(((PyObject *)__pyx_n_s__collections), ((PyObject *)__pyx_t_1), -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__namedtuple); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__namedtuple); + if (__pyx_t_1 == NULL) { + if (PyErr_ExceptionMatches(PyExc_AttributeError)) __Pyx_RaiseImportError(__pyx_n_s__namedtuple); + if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__namedtuple, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__defaultdict); + if (__pyx_t_1 == NULL) { + if (PyErr_ExceptionMatches(PyExc_AttributeError)) __Pyx_RaiseImportError(__pyx_n_s__defaultdict); + if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__defaultdict, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -24256,14 +26553,18 @@ PyMODINIT_FUNC PyInit_cvcf(void) * */ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(((PyObject *)__pyx_n_s__itemgetter)); PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__itemgetter)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__itemgetter)); - __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__operator), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__operator), ((PyObject *)__pyx_t_2), -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__itemgetter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__itemgetter); + if (__pyx_t_2 == NULL) { + if (PyErr_ExceptionMatches(PyExc_AttributeError)) __Pyx_RaiseImportError(__pyx_n_s__itemgetter); + if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__itemgetter, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -24276,19 +26577,19 @@ PyMODINIT_FUNC PyInit_cvcf(void) * * cimport ctabix */ - __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sys, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__re), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__re), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__re, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__copy), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__copy), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__copy, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__bisect), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__bisect), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__bisect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -24300,7 +26601,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) * * gtsRegEx = re.compile("[|/\\\\]") */ - __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__pysam), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__pysam), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); 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__pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -24335,7 +26636,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_129), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_131), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (PyObject_SetAttr(__pyx_m, __pyx_n_s__alleleRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -24348,7 +26649,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) * # obtain sequence from .fa file, without truncation * if end<=start: return "" */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_4cvcf_get_sequence, NULL, __pyx_n_s__cvcf); 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goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_builtin_object); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_builtin_object); __Pyx_GIVEREF(__pyx_builtin_object); - __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s__cvcf); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s__cvcf); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VCF, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VCF, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - /* "cvcf.pyx":1118 + /* "cvcf.pyx":1155 * pos -= 1 * * __all__ = [ # <<<<<<<<<<<<<< * "VCF", "VCFRecord", ] * */ - __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(((PyObject *)__pyx_n_s__VCF)); PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__VCF)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__VCF)); __Pyx_INCREF(((PyObject *)__pyx_n_s__VCFRecord)); PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__VCFRecord)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__VCFRecord)); - if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; /* "cvcf.pyx":1 @@ -25275,20 +27574,13 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_GOTREF(((PyObject *)__pyx_t_2)); if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - - /* "ctabix.pxd":2 - * - * cdef extern from "string.h": # <<<<<<<<<<<<<< - * ctypedef int size_t - * void *memcpy(void *dst,void *src,size_t len) - */ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); if (__pyx_m) { - __Pyx_AddTraceback("init cvcf"); + __Pyx_AddTraceback("init cvcf", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_ImportError, "init cvcf"); @@ -25303,12 +27595,34 @@ PyMODINIT_FUNC PyInit_cvcf(void) } /* Runtime support code */ +#if CYTHON_REFNANNY +static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { + PyObject *m = NULL, *p = NULL; + 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) - PyErr_SetObject(PyExc_NameError, name); + if (!result) { + if (dict != __pyx_b) { + PyErr_Clear(); + result = PyObject_GetAttr(__pyx_b, name); + } + if (!result) { + PyErr_SetObject(PyExc_NameError, name); + } + } return result; } @@ -25320,8 +27634,7 @@ static void __Pyx_RaiseArgtupleInvalid( Py_ssize_t num_found) { Py_ssize_t num_expected; - const char *number, *more_or_less; - + const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; @@ -25332,14 +27645,10 @@ static void __Pyx_RaiseArgtupleInvalid( if (exact) { more_or_less = "exactly"; } - number = (num_expected == 1) ? "" : "s"; PyErr_Format(PyExc_TypeError, - #if PY_VERSION_HEX < 0x02050000 - "%s() takes %s %d positional argument%s (%d given)", - #else - "%s() takes %s %zd positional argument%s (%zd given)", - #endif - func_name, more_or_less, num_expected, number, num_found); + "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); } static void __Pyx_RaiseDoubleKeywordsError( @@ -25367,7 +27676,6 @@ static int __Pyx_ParseOptionalKeywords( 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++; @@ -25377,7 +27685,7 @@ static int __Pyx_ParseOptionalKeywords( #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { #else - if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) { + if (unlikely(!PyUnicode_Check(key))) { #endif goto invalid_keyword_type; } else { @@ -25393,7 +27701,6 @@ static int __Pyx_ParseOptionalKeywords( if (*name) { values[name-argnames] = value; } else { - /* unexpected keyword found */ for (name=argnames; name != first_kw_arg; name++) { if (**name == key) goto arg_passed_twice; #if PY_MAJOR_VERSION >= 3 @@ -25435,6 +27742,7 @@ bad: } + static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; PyObject *tmp_type, *tmp_value, *tmp_tb; @@ -25480,11 +27788,10 @@ bad: return -1; } - static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); - tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; @@ -25494,26 +27801,30 @@ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyOb 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) { +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); Py_XINCREF(value); Py_XINCREF(tb); - /* First, check the traceback argument, replacing None with NULL. */ if (tb == Py_None) { Py_DECREF(tb); tb = 0; @@ -25523,7 +27834,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { "raise: arg 3 must be a traceback or None"); goto raise_error; } - /* Next, replace a missing value with None */ if (value == NULL) { value = Py_None; Py_INCREF(value); @@ -25534,13 +27844,11 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { if (!PyType_Check(type)) #endif { - /* Raising an instance. The value should be a dummy. */ if (value != Py_None) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } - /* Normalize to raise , */ Py_DECREF(value); value = type; #if PY_VERSION_HEX < 0x02050000 @@ -25564,7 +27872,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { } #endif } - __Pyx_ErrRestore(type, value, tb); return; raise_error: @@ -25573,10 +27880,8 @@ raise_error: Py_XDECREF(tb); return; } - #else /* Python 3+ */ - -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { @@ -25586,7 +27891,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { } if (value == Py_None) value = 0; - if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, @@ -25600,9 +27904,29 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { "raise: exception class must be a subclass of BaseException"); goto bad; } - + if (cause) { + PyObject *fixed_cause; + if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } + else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } + else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + if (!value) { + value = PyObject_CallObject(type, NULL); + } + PyException_SetCause(value, fixed_cause); + } PyErr_SetObject(type, value); - if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; @@ -25612,7 +27936,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { Py_XDECREF(tmp_tb); } } - bad: return; } @@ -25645,50 +27968,39 @@ bad: return (double)-1; } +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, - #if PY_VERSION_HEX < 0x02050000 - "need more than %d value%s to unpack", (int)index, - #else - "need more than %zd value%s to unpack", index, - #endif - (index == 1) ? "" : "s"); + "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack", + index, (index == 1) ? "" : "s"); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, - #if PY_VERSION_HEX < 0x02050000 - "too many values to unpack (expected %d)", (int)expected); - #else - "too many values to unpack (expected %zd)", expected); - #endif -} - -static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) { - PyObject *item; - if (!(item = PyIter_Next(iter))) { - if (!PyErr_Occurred()) { - __Pyx_RaiseNeedMoreValuesError(index); - } - } - return item; + "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected); } -static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) { - PyObject *item; - if ((item = PyIter_Next(iter))) { - Py_DECREF(item); +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; + } else if (PyErr_Occurred()) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { + PyErr_Clear(); + return 0; + } else { + return -1; + } } - else if (!PyErr_Occurred()) - return 0; - else - return -1; + return 0; } static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { @@ -25699,6 +28011,11 @@ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) } + +static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { + PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); +} + static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; @@ -25708,7 +28025,6 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, Py_XINCREF(*value); Py_XINCREF(*tb); } - static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); @@ -25723,7 +28039,7 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) Py_XDECREF(tmp_tb); } -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) { +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; @@ -25747,8 +28063,44 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) { 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); @@ -25756,13 +28108,22 @@ bad: return module; } +static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) { +#if PY_MAJOR_VERSION < 3 + PyErr_Format(PyExc_ImportError, "cannot import name %.230s", + PyString_AsString(name)); +#else + PyErr_Format(PyExc_ImportError, "cannot import name %S", name); +#endif +} + static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; /* Default metaclass */ #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); - metaclass = PyObject_GetAttrString(base, "__class__"); + metaclass = PyObject_GetAttrString(base, (char *)"__class__"); if (!metaclass) { PyErr_Clear(); metaclass = (PyObject*) Py_TYPE(base); @@ -25786,10 +28147,8 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na PyObject *modname) { PyObject *result; PyObject *metaclass; - if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; - /* Python2 __metaclass__ */ metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { @@ -25802,44 +28161,363 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na return result; } - -static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) { - __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType); +static PyObject * +__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) +{ + if (op->func_doc == NULL && op->func.m_ml->ml_doc) { +#if PY_MAJOR_VERSION >= 3 + op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); +#else + op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); +#endif + } + if (op->func_doc == 0) { + Py_INCREF(Py_None); + return Py_None; + } + Py_INCREF(op->func_doc); + return op->func_doc; +} +static int +__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp = op->func_doc; + if (value == NULL) + op->func_doc = Py_None; /* Mark as deleted */ + else + op->func_doc = value; + Py_INCREF(op->func_doc); + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) +{ + if (op->func_name == NULL) { +#if PY_MAJOR_VERSION >= 3 + op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); +#else + op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); +#endif + } + Py_INCREF(op->func_name); + return op->func_name; +} +static int +__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; +#if PY_MAJOR_VERSION >= 3 + if (value == NULL || !PyUnicode_Check(value)) { +#else + if (value == NULL || !PyString_Check(value)) { +#endif + PyErr_SetString(PyExc_TypeError, + "__name__ must be set to a string object"); + return -1; + } + tmp = op->func_name; + Py_INCREF(value); + op->func_name = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) +{ + PyObject *self; + self = m->func_closure; + if (self == NULL) + self = Py_None; + Py_INCREF(self); + return self; +} +static PyObject * +__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) +{ + if (op->func_dict == NULL) { + op->func_dict = PyDict_New(); + if (op->func_dict == NULL) + return NULL; + } + Py_INCREF(op->func_dict); + return op->func_dict; +} +static int +__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) +{ + PyObject *tmp; + if (value == NULL) { + PyErr_SetString(PyExc_TypeError, + "function's dictionary may not be deleted"); + return -1; + } + if (!PyDict_Check(value)) { + PyErr_SetString(PyExc_TypeError, + "setting function's dictionary to a non-dict"); + return -1; + } + tmp = op->func_dict; + Py_INCREF(value); + op->func_dict = value; + Py_XDECREF(tmp); + return 0; +} +static PyObject * +__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) +{ + PyObject* dict = PyModule_GetDict(__pyx_m); + Py_XINCREF(dict); + return dict; +} +static PyObject * +__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) +{ + Py_INCREF(Py_None); + return Py_None; +} +static PyObject * +__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) +{ + PyObject* result = (op->func_code) ? op->func_code : Py_None; + Py_INCREF(result); + return result; +} +static PyObject * +__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) +{ + if (op->defaults_tuple) { + Py_INCREF(op->defaults_tuple); + return op->defaults_tuple; + } + if (op->defaults_getter) { + PyObject *res = op->defaults_getter((PyObject *) op); + if (res) { + Py_INCREF(res); + op->defaults_tuple = res; + } + return res; + } + Py_INCREF(Py_None); + return Py_None; +} +static PyGetSetDef __pyx_CyFunction_getsets[] = { + {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, + {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, + {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, + {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, + {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, + {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, + {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, + {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, + {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; +#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ +#define PY_WRITE_RESTRICTED WRITE_RESTRICTED +#endif +static PyMemberDef __pyx_CyFunction_members[] = { + {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, + {0, 0, 0, 0, 0} +}; +static PyObject * +__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) +{ +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromString(m->func.m_ml->ml_name); +#else + return PyString_FromString(m->func.m_ml->ml_name); +#endif +} +static PyMethodDef __pyx_CyFunction_methods[] = { + {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, + {0, 0, 0, 0} +}; +static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, + PyObject *closure, PyObject *module, PyObject* code) { + __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); if (op == NULL) return NULL; - op->func.m_ml = ml; - Py_XINCREF(self); - op->func.m_self = self; - Py_XINCREF(module); - op->func.m_module = module; - PyObject_GC_Track(op); - return (PyObject *)op; -} - -static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) { - PyObject_GC_UnTrack(m); - Py_XDECREF(m->func.m_self); - Py_XDECREF(m->func.m_module); + op->flags = flags; + op->func_weakreflist = NULL; + op->func.m_ml = ml; + op->func.m_self = (PyObject *) op; + Py_XINCREF(closure); + op->func_closure = closure; + Py_XINCREF(module); + op->func.m_module = module; + op->func_dict = NULL; + op->func_name = NULL; + op->func_doc = NULL; + op->func_classobj = NULL; + Py_XINCREF(code); + op->func_code = code; + op->defaults_pyobjects = 0; + op->defaults = NULL; + op->defaults_tuple = NULL; + op->defaults_getter = NULL; + PyObject_GC_Track(op); + return (PyObject *) op; +} +static int +__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) +{ + Py_CLEAR(m->func_closure); + Py_CLEAR(m->func.m_module); + Py_CLEAR(m->func_dict); + Py_CLEAR(m->func_name); + Py_CLEAR(m->func_doc); + Py_CLEAR(m->func_code); + Py_CLEAR(m->func_classobj); + Py_CLEAR(m->defaults_tuple); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_XDECREF(pydefaults[i]); + PyMem_Free(m->defaults); + m->defaults = NULL; + } + return 0; +} +static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) +{ + PyObject_GC_UnTrack(m); + if (m->func_weakreflist != NULL) + PyObject_ClearWeakRefs((PyObject *) m); + __Pyx_CyFunction_clear(m); PyObject_GC_Del(m); } - -static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) { - if (obj == Py_None) - obj = NULL; - return PyMethod_New(func, obj, type); +static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) +{ + Py_VISIT(m->func_closure); + Py_VISIT(m->func.m_module); + Py_VISIT(m->func_dict); + Py_VISIT(m->func_name); + Py_VISIT(m->func_doc); + Py_VISIT(m->func_code); + Py_VISIT(m->func_classobj); + Py_VISIT(m->defaults_tuple); + if (m->defaults) { + PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); + int i; + for (i = 0; i < m->defaults_pyobjects; i++) + Py_VISIT(pydefaults[i]); + } + return 0; } - -static int __pyx_binding_PyCFunctionType_init(void) { - __pyx_binding_PyCFunctionType_type = PyCFunction_Type; - __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method"); - __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc; - __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get; - if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) { +static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) +{ + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { + Py_INCREF(func); + return func; + } + if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { + if (type == NULL) + type = (PyObject *)(Py_TYPE(obj)); + return PyMethod_New(func, + type, (PyObject *)(Py_TYPE(type))); + } + if (obj == Py_None) + obj = NULL; + return PyMethod_New(func, obj, type); +} +static PyObject* +__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) +{ + PyObject *func_name = __Pyx_CyFunction_get_name(op); +#if PY_MAJOR_VERSION >= 3 + return PyUnicode_FromFormat("", + func_name, (void *)op); +#else + return PyString_FromFormat("", + PyString_AsString(func_name), (void *)op); +#endif +} +static PyTypeObject __pyx_CyFunctionType_type = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ + sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ +#if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ +#else + 0, /*reserved*/ +#endif + (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + __Pyx_PyCFunction_Call, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ + 0, /*tp_doc*/ + (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ + (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ + 0, /*tp_richcompare*/ + offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_CyFunction_methods, /*tp_methods*/ + __pyx_CyFunction_members, /*tp_members*/ + __pyx_CyFunction_getsets, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + __Pyx_CyFunction_descr_get, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + 0, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ +#if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ +#endif +}; +static int __Pyx_CyFunction_init(void) +{ + if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; - } - __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type; + __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; - +} +void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) +{ + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults = PyMem_Malloc(size); + if (!m->defaults) + return PyErr_NoMemory(); + memset(m->defaults, 0, sizeof(size)); + m->defaults_pyobjects = pyobjects; + return m->defaults; +} +static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) +{ + __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; + m->defaults_tuple = tuple; + Py_INCREF(tuple); } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { @@ -25862,11 +28540,83 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; - return _PyLong_FromByteArray(bytes, sizeof(uint32_t), + return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { + return (equals == Py_NE); + } else if (PyBytes_GET_SIZE(s1) == 1) { + if (equals == Py_EQ) + return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]); + else + return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]); + } else { + int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1)); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +} + +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { + #if CYTHON_PEP393_ENABLED + if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) + return -1; + if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { + return (equals == Py_NE); + } else if (PyUnicode_GET_LENGTH(s1) == 1) { + Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); + Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); + return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); + #else + if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { + return (equals == Py_NE); + } else if (PyUnicode_GET_SIZE(s1) == 1) { + Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; + Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; + return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); + #endif + } else { + int result = PyUnicode_Compare(s1, s2); + if ((result == -1) && unlikely(PyErr_Occurred())) + return -1; + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +} + static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; @@ -26078,9 +28828,9 @@ static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { "can't convert negative value to unsigned long"); return (unsigned long)-1; } - return PyLong_AsUnsignedLong(x); + return (unsigned long)PyLong_AsUnsignedLong(x); } else { - return PyLong_AsLong(x); + return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; @@ -26113,9 +28863,9 @@ static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObje "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } - return PyLong_AsUnsignedLongLong(x); + return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { - return PyLong_AsLongLong(x); + return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; @@ -26148,9 +28898,9 @@ static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { "can't convert negative value to long"); return (long)-1; } - return PyLong_AsUnsignedLong(x); + return (long)PyLong_AsUnsignedLong(x); } else { - return PyLong_AsLong(x); + return (long)PyLong_AsLong(x); } } else { long val; @@ -26183,9 +28933,9 @@ static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } - return PyLong_AsUnsignedLongLong(x); + return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { - return PyLong_AsLongLong(x); + return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; @@ -26218,9 +28968,9 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { "can't convert negative value to signed long"); return (signed long)-1; } - return PyLong_AsUnsignedLong(x); + return (signed long)PyLong_AsUnsignedLong(x); } else { - return PyLong_AsLong(x); + return (signed long)PyLong_AsLong(x); } } else { signed long val; @@ -26253,9 +29003,9 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } - return PyLong_AsUnsignedLongLong(x); + return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { - return PyLong_AsLongLong(x); + return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; @@ -26267,24 +29017,325 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* } } +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} + +static PyObject *__Pyx_Generator_Next(PyObject *self); +static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); +static PyObject *__Pyx_Generator_Close(PyObject *self); +static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); +static CYTHON_INLINE +void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) +{ + PyObject *exc_type = self->exc_type; + PyObject *exc_value = self->exc_value; + PyObject *exc_traceback = self->exc_traceback; + self->exc_type = NULL; + self->exc_value = NULL; + self->exc_traceback = NULL; + Py_XDECREF(exc_type); + Py_XDECREF(exc_value); + Py_XDECREF(exc_traceback); +} +static CYTHON_INLINE +PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) +{ + PyObject *retval; + if (unlikely(self->is_running)) { + PyErr_SetString(PyExc_ValueError, + "generator already executing"); + return NULL; + } + if (unlikely(self->resume_label == 0)) { + if (unlikely(value && value != Py_None)) { + PyErr_SetString(PyExc_TypeError, + "can't send non-None value to a " + "just-started generator"); + return NULL; + } + } + if (unlikely(self->resume_label == -1)) { + PyErr_SetNone(PyExc_StopIteration); + return NULL; + } + if (value) + __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); + else + __Pyx_Generator_ExceptionClear(self); + self->is_running = 1; + retval = self->body((PyObject *) self, value); + self->is_running = 0; + if (retval) + __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); + else + __Pyx_Generator_ExceptionClear(self); + return retval; +} +static PyObject *__Pyx_Generator_Next(PyObject *self) +{ + return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None); +} +static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) +{ + return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value); +} +static PyObject *__Pyx_Generator_Close(PyObject *self) +{ + __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; + PyObject *retval; +#if PY_VERSION_HEX < 0x02050000 + PyErr_SetNone(PyExc_StopIteration); +#else + PyErr_SetNone(PyExc_GeneratorExit); +#endif + retval = __Pyx_Generator_SendEx(generator, NULL); + if (retval) { + Py_DECREF(retval); + PyErr_SetString(PyExc_RuntimeError, + "generator ignored GeneratorExit"); + return NULL; + } +#if PY_VERSION_HEX < 0x02050000 + if (PyErr_ExceptionMatches(PyExc_StopIteration)) +#else + if (PyErr_ExceptionMatches(PyExc_StopIteration) + || PyErr_ExceptionMatches(PyExc_GeneratorExit)) +#endif + { + PyErr_Clear(); /* ignore these errors */ + Py_INCREF(Py_None); + return Py_None; + } + return NULL; +} +static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) +{ + __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; + PyObject *typ; + PyObject *tb = NULL; + PyObject *val = NULL; + if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) + return NULL; + __Pyx_Raise(typ, val, tb, NULL); + return __Pyx_Generator_SendEx(generator, NULL); +} +static int +__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) +{ + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; + Py_VISIT(gen->closure); + Py_VISIT(gen->classobj); + Py_VISIT(gen->exc_type); + Py_VISIT(gen->exc_value); + Py_VISIT(gen->exc_traceback); + return 0; +} +static void +__Pyx_Generator_dealloc(PyObject *self) +{ + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; + PyObject_GC_UnTrack(gen); + if (gen->gi_weakreflist != NULL) + PyObject_ClearWeakRefs(self); + PyObject_GC_Track(self); + if (gen->resume_label > 0) { + Py_TYPE(gen)->tp_del(self); + if (self->ob_refcnt > 0) + return; /* resurrected. :( */ + } + PyObject_GC_UnTrack(self); + Py_CLEAR(gen->closure); + Py_CLEAR(gen->classobj); + Py_CLEAR(gen->exc_type); + Py_CLEAR(gen->exc_value); + Py_CLEAR(gen->exc_traceback); + PyObject_GC_Del(gen); +} +static void +__Pyx_Generator_del(PyObject *self) +{ + PyObject *res; + PyObject *error_type, *error_value, *error_traceback; + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; + if (gen->resume_label <= 0) + return ; + assert(self->ob_refcnt == 0); + self->ob_refcnt = 1; + __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); + res = __Pyx_Generator_Close(self); + if (res == NULL) + PyErr_WriteUnraisable(self); + else + Py_DECREF(res); + __Pyx_ErrRestore(error_type, error_value, error_traceback); + /* Undo the temporary resurrection; can't use DECREF here, it would + * cause a recursive call. + */ + assert(self->ob_refcnt > 0); + if (--self->ob_refcnt == 0) + return; /* this is the normal path out */ + /* close() resurrected it! Make it look like the original Py_DECREF + * never happened. + */ + { + Py_ssize_t refcnt = self->ob_refcnt; + _Py_NewReference(self); + self->ob_refcnt = refcnt; + } + assert(PyType_IS_GC(self->ob_type) && + _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); + /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so + * we need to undo that. */ + _Py_DEC_REFTOTAL; + /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object + * chain, so no more to do there. + * If COUNT_ALLOCS, the original decref bumped tp_frees, and + * _Py_NewReference bumped tp_allocs: both of those need to be + * undone. + */ +#ifdef COUNT_ALLOCS + --self->ob_type->tp_frees; + --self->ob_type->tp_allocs; +#endif +} +static PyMemberDef __pyx_Generator_memberlist[] = { + {(char *) "gi_running", + T_INT, + offsetof(__pyx_GeneratorObject, is_running), + READONLY, + NULL}, + {0, 0, 0, 0, 0} +}; +static PyMethodDef __pyx_Generator_methods[] = { + {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0}, + {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0}, + {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, + {0, 0, 0, 0} +}; +static PyTypeObject __pyx_GeneratorType = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("generator"), /*tp_name*/ + sizeof(__pyx_GeneratorObject), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ +#if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ +#else + 0, /*reserved*/ +#endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + PyObject_GenericGetAttr, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ + 0, /*tp_doc*/ + (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */ + PyObject_SelfIter, /*tp_iter*/ + (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/ + __pyx_Generator_methods, /*tp_methods*/ + __pyx_Generator_memberlist, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + 0, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + __Pyx_Generator_del, /*tp_del*/ +#if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ +#endif +}; +static +__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, + PyObject *closure) +{ + __pyx_GeneratorObject *gen = + PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType); + if (gen == NULL) + return NULL; + gen->body = body; + gen->closure = closure; + Py_XINCREF(closure); + gen->is_running = 0; + gen->resume_label = 0; + gen->classobj = NULL; + gen->exc_type = NULL; + gen->exc_value = NULL; + gen->exc_traceback = NULL; + gen->gi_weakreflist = NULL; + PyObject_GC_Track(gen); + return gen; +} +static int __pyx_Generator_init(void) +{ + return PyType_Ready(&__pyx_GeneratorType); +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + #if PY_VERSION_HEX < 0x02050000 + return PyErr_Warn(NULL, message); + #else + return PyErr_WarnEx(NULL, message, 1); + #endif + } + return 0; +} + #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, - long size, int strict) + size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; - py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; - #if PY_MAJOR_VERSION < 3 - py_name = PyString_FromString(class_name); - #else - py_name = PyUnicode_FromString(class_name); - #endif + py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); @@ -26300,17 +29351,17 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class module_name, class_name); goto bad; } - if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) { + if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 - PyErr_Warn(NULL, warning); + if (PyErr_Warn(NULL, warning) < 0) goto bad; #else - PyErr_WarnEx(NULL, warning, 0); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } - else if (((PyTypeObject *)result)->tp_basicsize != size) { + else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); @@ -26320,7 +29371,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class bad: Py_XDECREF(py_module); Py_XDECREF(result); - return 0; + return NULL; } #endif @@ -26329,12 +29380,7 @@ bad: static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; - - #if PY_MAJOR_VERSION < 3 - py_name = PyString_FromString(name); - #else - py_name = PyUnicode_FromString(name); - #endif + py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); @@ -26382,28 +29428,105 @@ bad: return -1; } +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + #include "compile.h" #include "frameobject.h" #include "traceback.h" - -static void __Pyx_AddTraceback(const char *funcname) { +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; - PyObject *py_globals = 0; - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - #if PY_MAJOR_VERSION < 3 - py_srcfile = PyString_FromString(__pyx_filename); + py_srcfile = PyString_FromString(filename); #else - py_srcfile = PyUnicode_FromString(__pyx_filename); + py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; - if (__pyx_clineno) { + if (c_line) { #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { @@ -26414,28 +29537,45 @@ static void __Pyx_AddTraceback(const char *funcname) { #endif } if (!py_funcname) goto bad; - py_globals = PyModule_GetDict(__pyx_m); - if (!py_globals) goto bad; - py_code = PyCode_New( + py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ - #if PY_MAJOR_VERSION >= 3 0, /*int kwonlyargcount,*/ - #endif 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ - __pyx_lineno, /*int firstlineno,*/ + py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); - if (!py_code) goto bad; + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_globals = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_globals = PyModule_GetDict(__pyx_m); + if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ @@ -26443,11 +29583,9 @@ static void __Pyx_AddTraceback(const char *funcname) { 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; - py_frame->f_lineno = __pyx_lineno; + py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); Py_XDECREF(py_code); Py_XDECREF(py_frame); } @@ -26482,6 +29620,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { return 0; } + /* Type Conversion Functions */ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {