-/* 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 <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#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
#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
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#endif
+
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
+
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define 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)
#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 <math.h>
+#define __PYX_HAVE__cvcf
#define __PYX_HAVE_API__cvcf
#include "stdlib.h"
#include "string.h"
#include "unistd.h"
#include "bgzf.h"
#include "tabix.h"
+#ifdef _OPENMP
+#include <omp.h>
+#endif /* _OPENMP */
#ifdef PYREX_WITHOUT_ASSERTIONS
#define CYTHON_WITHOUT_ASSERTIONS
# 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
#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
+#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
static CYTHON_INLINE 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;
"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;
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;
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
* ###########################################################################################################
*
* '''vcf record.
*
*/
-
struct __pyx_obj_4cvcf_VCFRecord {
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
PyObject *vcf;
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 )
*
*
* 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: # <<<<<<<<<<<<<<
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
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) : # <<<<<<<<<<<<<<
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 )
*
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;
static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
-/* "TabProxies.pxd":80
+/* "TabProxies.pxd":72
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
};
static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
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#define CYTHON_REFNANNY 0
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void (*INCREF)(void*, PyObject*, int);
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static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
- static __Pyx_RefNannyAPIStruct * __Pyx_RefNannyImportAPI(const char *modname) {
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- m = PyImport_ImportModule((char *)modname);
- if (!m) goto end;
- p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
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- r = PyLong_AsVoidPtr(p);
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- Py_XDECREF(p);
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- #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;
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)))) {
}
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)))) {
}
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*/
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);
#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);
}
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 */
#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;
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 <structmember.h>
+#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 <string.h>
-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 *);
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 <structmember.h>
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+typedef struct {
+ PyObject_HEAD
+ __pyx_generator_body_t body;
+ PyObject *closure;
+ int is_running;
+ int resume_label;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+ PyObject *gi_weakreflist;
+ PyObject *classobj;
+} __pyx_GeneratorObject;
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure);
+static int __pyx_Generator_init(void);
+
+static int __Pyx_check_binary_version(void);
+
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
static 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[] = ":";
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[] = "<none>";
-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";
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";
static char __pyx_k___copy[] = "_copy";
static char __pyx_k___info[] = "_info";
static char __pyx_k___line[] = "_line";
+static char __pyx_k__addns[] = "addns";
+static char __pyx_k__blurp[] = "blurp";
static char __pyx_k__chrom[] = "chrom";
static char __pyx_k__descr[] = "descr";
static char __pyx_k__error[] = "error";
+static char __pyx_k__faref[] = "faref";
static char __pyx_k__fetch[] = "fetch";
+static char __pyx_k__first[] = "first";
+static char __pyx_k__ielts[] = "ielts";
+static char __pyx_k__label[] = "label";
static char __pyx_k__lines[] = "lines";
static char __pyx_k__match[] = "match";
static char __pyx_k__parse[] = "parse";
static char __pyx_k__pysam[] = "pysam";
static char __pyx_k__range[] = "range";
+static char __pyx_k__sdata[] = "sdata";
static char __pyx_k__split[] = "split";
static char __pyx_k__start[] = "start";
static char __pyx_k__strip[] = "strip";
static char __pyx_k__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__";
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";
static char __pyx_k___version[] = "_version";
static char __pyx_k__deepcopy[] = "deepcopy";
static char __pyx_k__endswith[] = "endswith";
+static char __pyx_k__expected[] = "expected";
static char __pyx_k__filename[] = "filename";
static char __pyx_k__gtsRegEx[] = "gtsRegEx";
+static char __pyx_k__headings[] = "headings";
static char __pyx_k__inregion[] = "inregion";
static char __pyx_k__operator[] = "operator";
+static char __pyx_k__required[] = "required";
+static char __pyx_k__sequence[] = "sequence";
+static char __pyx_k__shortest[] = "shortest";
static char __pyx_k__validate[] = "validate";
static char __pyx_k__Character[] = "Character";
static char __pyx_k__NT_NUMBER[] = "NT_NUMBER";
static char __pyx_k__getfilter[] = "getfilter";
static char __pyx_k__getformat[] = "getformat";
static char __pyx_k__getheader[] = "getheader";
+static char __pyx_k__last_line[] = "last_line";
static char __pyx_k__leftalign[] = "leftalign";
static char __pyx_k__lineparse[] = "lineparse";
static char __pyx_k__reference[] = "reference";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___leftalign[] = "_leftalign";
static char __pyx_k___reference[] = "_reference";
+static char __pyx_k__errorlabel[] = "errorlabel";
static char __pyx_k__fileformat[] = "fileformat";
static char __pyx_k__formatdict[] = "formatdict";
static char __pyx_k__getsamples[] = "getsamples";
static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
static char __pyx_k___sample2column[] = "_sample2column";
+static char __pyx_k__have_deletions[] = "have_deletions";
static char __pyx_k___add_definition[] = "_add_definition";
static char __pyx_k___ignored_errors[] = "_ignored_errors";
+static char __pyx_k__faref_leftflank[] = "faref_leftflank";
static char __pyx_k__POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE";
static char __pyx_k__parse_formatdata[] = "parse_formatdata";
static char __pyx_k__ERROR_INFO_STRING[] = "ERROR_INFO_STRING";
static char __pyx_k__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;
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;
static PyObject *__pyx_n_s__D;
static PyObject *__pyx_n_s__DP;
static PyObject *__pyx_n_s__Description;
+static PyObject *__pyx_n_s__EC;
static PyObject *__pyx_n_s__ERROR_INFO_STRING;
static PyObject *__pyx_n_s__ERROR_TRAILING_DATA;
static PyObject *__pyx_n_s__ERROR_UNKNOWN_KEY;
static PyObject *__pyx_n_s__FT;
static PyObject *__pyx_n_s__Flag;
static PyObject *__pyx_n_s__Float;
+static PyObject *__pyx_n_s__G;
+static PyObject *__pyx_n_s__GL;
+static PyObject *__pyx_n_s__GLE;
+static PyObject *__pyx_n_s__GP;
static PyObject *__pyx_n_s__GQ;
static PyObject *__pyx_n_s__GT;
static PyObject *__pyx_n_s__GTdata;
static PyObject *__pyx_n_s__Integer;
static PyObject *__pyx_n_s__KeyError;
static PyObject *__pyx_n_s__MISSING_REF;
+static PyObject *__pyx_n_s__MQ;
static PyObject *__pyx_n_s__N;
static PyObject *__pyx_n_s__NT_ALLELES;
static PyObject *__pyx_n_s__NT_GENOTYPES;
static PyObject *__pyx_n_s__Number;
static PyObject *__pyx_n_b__PASS;
static PyObject *__pyx_n_s__PASS;
+static PyObject *__pyx_n_s__PL;
static PyObject *__pyx_n_s__POS;
static PyObject *__pyx_n_s__POS_NOT_NUMERICAL;
static PyObject *__pyx_n_s__POS_NOT_POSITIVE;
+static PyObject *__pyx_n_s__PQ;
+static PyObject *__pyx_n_s__PS;
static PyObject *__pyx_n_s__QUAL;
static PyObject *__pyx_n_s__QUAL_NOT_NUMERICAL;
static PyObject *__pyx_n_s__REF;
static PyObject *__pyx_n_s___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;
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;
static PyObject *__pyx_n_s__pos2;
static PyObject *__pyx_n_s__pysam;
static PyObject *__pyx_n_s__qual;
+static PyObject *__pyx_n_s__r;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_n_s__re;
static PyObject *__pyx_n_s__record;
static PyObject *__pyx_n_s__region;
static PyObject *__pyx_n_s__regions;
static PyObject *__pyx_n_s__replace;
+static PyObject *__pyx_n_s__required;
+static PyObject *__pyx_n_s__rest;
+static PyObject *__pyx_n_s__result;
+static PyObject *__pyx_n_s__s;
+static PyObject *__pyx_n_s__sample;
static PyObject *__pyx_n_s__samples;
+static PyObject *__pyx_n_s__sdata;
static PyObject *__pyx_n_s__self;
static PyObject *__pyx_n_s__separator;
+static PyObject *__pyx_n_s__sequence;
static PyObject *__pyx_n_s__setfilter;
static PyObject *__pyx_n_s__setformat;
static PyObject *__pyx_n_s__setheader;
static PyObject *__pyx_n_s__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;
static PyObject *__pyx_n_s__write_header;
static PyObject *__pyx_n_s__write_heading;
static PyObject *__pyx_n_s__writeheader;
+static PyObject *__pyx_n_s__x;
+static PyObject *__pyx_n_s__y;
static PyObject *__pyx_n_s__zip;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_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;
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;
+static PyObject *__pyx_k_codeobj_209;
+static PyObject *__pyx_k_codeobj_211;
+static PyObject *__pyx_k_codeobj_213;
+static PyObject *__pyx_k_codeobj_215;
+static PyObject *__pyx_k_codeobj_217;
+static PyObject *__pyx_k_codeobj_219;
+static PyObject *__pyx_k_codeobj_221;
+static PyObject *__pyx_k_codeobj_223;
+static PyObject *__pyx_k_codeobj_225;
+static PyObject *__pyx_k_codeobj_227;
+static PyObject *__pyx_k_codeobj_229;
+static PyObject *__pyx_k_codeobj_231;
+static PyObject *__pyx_k_codeobj_233;
+static PyObject *__pyx_k_codeobj_235;
+static PyObject *__pyx_k_codeobj_237;
+static PyObject *__pyx_k_codeobj_239;
+static PyObject *__pyx_k_codeobj_241;
+static PyObject *__pyx_k_codeobj_243;
+static PyObject *__pyx_k_codeobj_245;
+static PyObject *__pyx_k_codeobj_247;
+static PyObject *__pyx_k_codeobj_249;
+static PyObject *__pyx_k_codeobj_251;
+static PyObject *__pyx_k_codeobj_253;
+static PyObject *__pyx_k_codeobj_255;
+static PyObject *__pyx_k_codeobj_258;
+
+/* Python wrapper */
+static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_1get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pw_4cvcf_1get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
+static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_chrom = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_fa = 0;
- PyObject *__pyx_v_sequence;
- PyObject *__pyx_r = NULL;
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- int __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- Py_ssize_t __pyx_t_7;
static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
- __Pyx_RefNannySetupContext("get_sequence");
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("get_sequence (wrapper)", 0);
__pyx_self = __pyx_self;
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
+ {
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);
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*/
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__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;}
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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;
"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);
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 <class>, <instance> */
Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
}
#endif
}
-
__Pyx_ErrRestore(type, value, tb);
return;
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)) {
}
if (value == Py_None)
value = 0;
-
if (PyExceptionInstance_Check(type)) {
if (value) {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
-
+ if (cause) {
+ PyObject *fixed_cause;
+ if (PyExceptionClass_Check(cause)) {
+ fixed_cause = PyObject_CallObject(cause, NULL);
+ if (fixed_cause == NULL)
+ goto bad;
+ }
+ else if (PyExceptionInstance_Check(cause)) {
+ fixed_cause = cause;
+ Py_INCREF(fixed_cause);
+ }
+ else {
+ PyErr_SetString(PyExc_TypeError,
+ "exception causes must derive from "
+ "BaseException");
+ goto bad;
+ }
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
+ PyException_SetCause(value, fixed_cause);
+ }
PyErr_SetObject(type, value);
-
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
Py_XDECREF(tmp_tb);
}
}
-
bad:
return;
}
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) {
}
+
+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;
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();
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;
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);
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);
PyObject *modname) {
PyObject *result;
PyObject *metaclass;
-
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
-
/* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
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("<cyfunction %U at %p>",
+ func_name, (void *)op);
+#else
+ return PyString_FromFormat("<cyfunction %s at %p>",
+ 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) {
} 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;
"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;
"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;
"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;
"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;
"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;
"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;
}
}
+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);
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);
bad:
Py_XDECREF(py_module);
Py_XDECREF(result);
- return 0;
+ return NULL;
}
#endif
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);
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 {
#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,*/
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);
}
return 0;
}
+
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
projects / pysam.git / blobdiff