--- /dev/null
+/* Generated by Cython 0.13 on Thu May 5 15:40:49 2011 */
+
+#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.
+#else
+
+#include <stddef.h> /* For offsetof */
+#ifndef offsetof
+#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
+#endif
+
+#if !defined(WIN32) && !defined(MS_WINDOWS)
+ #ifndef __stdcall
+ #define __stdcall
+ #endif
+ #ifndef __cdecl
+ #define __cdecl
+ #endif
+ #ifndef __fastcall
+ #define __fastcall
+ #endif
+#endif
+
+#ifndef DL_IMPORT
+ #define DL_IMPORT(t) t
+#endif
+#ifndef DL_EXPORT
+ #define DL_EXPORT(t) t
+#endif
+
+#ifndef PY_LONG_LONG
+ #define PY_LONG_LONG LONG_LONG
+#endif
+
+#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)
+#endif
+
+#if PY_VERSION_HEX < 0x02050000
+ typedef int Py_ssize_t;
+ #define PY_SSIZE_T_MAX INT_MAX
+ #define PY_SSIZE_T_MIN INT_MIN
+ #define PY_FORMAT_SIZE_T ""
+ #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) PyInt_AsLong(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)
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+
+ typedef struct {
+ void *buf;
+ PyObject *obj;
+ Py_ssize_t len;
+ Py_ssize_t itemsize;
+ int readonly;
+ int ndim;
+ char *format;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ void *internal;
+ } Py_buffer;
+
+ #define PyBUF_SIMPLE 0
+ #define PyBUF_WRITABLE 0x0001
+ #define PyBUF_FORMAT 0x0004
+ #define PyBUF_ND 0x0008
+ #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+
+#endif
+
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+#else
+ #define __Pyx_BUILTIN_MODULE_NAME "builtins"
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define Py_TPFLAGS_CHECKTYPES 0
+ #define Py_TPFLAGS_HAVE_INDEX 0
+#endif
+
+#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
+ #define Py_TPFLAGS_HAVE_NEWBUFFER 0
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyBaseString_Type PyUnicode_Type
+ #define PyStringObject PyUnicodeObject
+ #define PyString_Type PyUnicode_Type
+ #define PyString_Check PyUnicode_Check
+ #define PyString_CheckExact PyUnicode_CheckExact
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
+ #define PyBytesObject PyStringObject
+ #define PyBytes_Type PyString_Type
+ #define PyBytes_Check PyString_Check
+ #define PyBytes_CheckExact PyString_CheckExact
+ #define PyBytes_FromString PyString_FromString
+ #define PyBytes_FromStringAndSize PyString_FromStringAndSize
+ #define PyBytes_FromFormat PyString_FromFormat
+ #define PyBytes_DecodeEscape PyString_DecodeEscape
+ #define PyBytes_AsString PyString_AsString
+ #define PyBytes_AsStringAndSize PyString_AsStringAndSize
+ #define PyBytes_Size PyString_Size
+ #define PyBytes_AS_STRING PyString_AS_STRING
+ #define PyBytes_GET_SIZE PyString_GET_SIZE
+ #define PyBytes_Repr PyString_Repr
+ #define PyBytes_Concat PyString_Concat
+ #define PyBytes_ConcatAndDel PyString_ConcatAndDel
+ #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
+ #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
+#endif
+
+#ifndef PySet_CheckExact
+# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyInt_Type PyLong_Type
+ #define PyInt_Check(op) PyLong_Check(op)
+ #define PyInt_CheckExact(op) PyLong_CheckExact(op)
+ #define PyInt_FromString PyLong_FromString
+ #define PyInt_FromUnicode PyLong_FromUnicode
+ #define PyInt_FromLong PyLong_FromLong
+ #define PyInt_FromSize_t PyLong_FromSize_t
+ #define PyInt_FromSsize_t PyLong_FromSsize_t
+ #define PyInt_AsLong PyLong_AsLong
+ #define PyInt_AS_LONG PyLong_AS_LONG
+ #define PyInt_AsSsize_t PyLong_AsSsize_t
+ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
+ #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyBoolObject PyLongObject
+#endif
+
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
+#endif
+
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
+#else
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
+ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
+#endif
+
+#if PY_VERSION_HEX < 0x02050000
+ #define __Pyx_NAMESTR(n) ((char *)(n))
+ #define __Pyx_DOCSTR(n) ((char *)(n))
+#else
+ #define __Pyx_NAMESTR(n) (n)
+ #define __Pyx_DOCSTR(n) (n)
+#endif
+
+#ifdef __cplusplus
+#define __PYX_EXTERN_C extern "C"
+#else
+#define __PYX_EXTERN_C extern
+#endif
+
+#if defined(WIN32) || defined(MS_WINDOWS)
+#define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+#define __PYX_HAVE_API__cvcf
+#include "stdlib.h"
+#include "string.h"
+#include "stdint.h"
+#include "stdio.h"
+#include "ctype.h"
+#include "sys/types.h"
+#include "sys/stat.h"
+#include "fcntl.h"
+#include "unistd.h"
+#include "bgzf.h"
+#include "tabix.h"
+
+/* inline attribute */
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
+
+/* unused attribute */
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || defined(__INTEL_COMPILER)
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+
+typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+
+/* Type Conversion Predeclarations */
+
+#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
+#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
+
+#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
+
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
+
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+
+
+#ifdef __GNUC__
+/* Test for GCC > 2.95 */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#define likely(x) __builtin_expect(!!(x), 1)
+#define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* __GNUC__ > 2 ... */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ */
+
+static PyObject *__pyx_m;
+static PyObject *__pyx_b;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+
+
+static const char *__pyx_f[] = {
+ "cvcf.pyx",
+ "ctabix.pxd",
+ "TabProxies.pxd",
+};
+
+/* Type declarations */
+
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
+ *
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_TupleProxy {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
+ char *data;
+ char **fields;
+ int nfields;
+ int index;
+ int nbytes;
+ int offset;
+ int is_modified;
+};
+
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_obj_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+};
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_BedProxy {
+ struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+ * ###########################################################################################################
+ *
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_obj_4cvcf_VCFRecord {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+ PyObject *vcf;
+ char *contig;
+ uint32_t pos;
+};
+
+/* "pysam/TabProxies.pxd":91
+ * 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;
+};
+
+/* "pysam/ctabix.pxd":178
+ * cdef tabix_t * tabixfile
+ *
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
+ */
+
+struct __pyx_obj_6ctabix_Parser {
+ PyObject_HEAD
+};
+
+/* "pysam/TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * 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;
+ int hasOwnAttributes;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221
+ *
+ *
+ * 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;
+};
+
+/* "pysam/ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+ *
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef char * filename
+ *
+ */
+
+struct __pyx_obj_6ctabix_Tabixfile {
+ PyObject_HEAD
+ char *filename;
+ tabix_t *tabixfile;
+};
+
+
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
+ *
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_TupleProxy {
+ int (*getMaxFields)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t);
+ PyObject *(*take)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*present)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*copy)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*update)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
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+static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+
+
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+
+
+/* "pysam/TabProxies.pxd":91
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+
+
+/* "pysam/TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+ * ###########################################################################################################
+ *
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_vtabstruct_4cvcf_VCFRecord {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
+
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_BedProxy {
+ 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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+ typedef struct {
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+ void (*DECREF)(void*, PyObject*, int);
+ void (*GOTREF)(void*, PyObject*, int);
+ void (*GIVEREF)(void*, PyObject*, int);
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+ #define __Pyx_GIVEREF(r)
+ #define __Pyx_XDECREF(r) Py_XDECREF(r)
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+#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0)
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+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
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+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_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 int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
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+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
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+}
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+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ 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);
+ }
+ 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 {
+ r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ }
+ return r;
+}
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*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))
+
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
+
+#if PY_MAJOR_VERSION >= 3
+static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
+ PyObject *value;
+ if (unlikely(d == Py_None)) {
+ __Pyx_RaiseNoneIndexingError();
+ return NULL;
+ }
+ value = PyDict_GetItemWithError(d, key);
+ if (unlikely(!value)) {
+ if (!PyErr_Occurred())
+ PyErr_SetObject(PyExc_KeyError, key);
+ return NULL;
+ }
+ Py_INCREF(value);
+ return value;
+}
+#else
+ #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
+#endif
+
+static CYTHON_INLINE long __Pyx_NegateNonNeg(long 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_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+
+static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */
+
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
+ if (likely(PyList_CheckExact(L))) {
+ if (PyList_Append(L, x) < 0) return NULL;
+ Py_INCREF(Py_None);
+ return Py_None; /* this is just to have an accurate signature */
+ }
+ else {
+ PyObject *r, *m;
+ m = __Pyx_GetAttrString(L, "append");
+ if (!m) return NULL;
+ r = PyObject_CallFunctionObjArgs(m, x, NULL);
+ Py_DECREF(m);
+ return r;
+ }
+}
+
+#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_SetItemInt_Fast(o, i, v) : \
+ __Pyx_SetItemInt_Generic(o, to_py_func(i), v))
+
+static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
+ int r;
+ if (!j) return -1;
+ r = PyObject_SetItem(o, j, v);
+ Py_DECREF(j);
+ return r;
+}
+
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
+ if (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 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) */
+
+#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;
+
+#define PySet_Type (*__Pyx_PySet_Type)
+#define PyFrozenSet_Type (*__Pyx_PyFrozenSet_Type)
+
+#define PyAnySet_Check(ob) \
+ (PyAnySet_CheckExact(ob) || \
+ PyType_IsSubtype((ob)->ob_type, &PySet_Type) || \
+ PyType_IsSubtype((ob)->ob_type, &PyFrozenSet_Type))
+
+#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_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*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 CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+/* Module declarations from ctabix */
+
+static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_Parser = 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 */
+
+static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0;
+static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0;
+#define __Pyx_MODULE_NAME "cvcf"
+int __pyx_module_is_main_cvcf = 0;
+
+/* 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 char __pyx_k_1[] = "";
+static char __pyx_k_2[] = ",";
+static char __pyx_k_3[] = ":";
+static char __pyx_k_4[] = "-";
+static char __pyx_k_5[] = "Don't understand region string '%s'";
+static char __pyx_k_6[] = ".";
+static char __pyx_k_7[] = ";";
+static char __pyx_k_8[] = "=";
+static char __pyx_k_9[] = "BAD_NUMBER_OF_VALUES";
+static char __pyx_k_10[] = "(found %s values in element %s; expected %s)";
+static char __pyx_k_11[] = "BAD_NUMBER_OF_PARAMETERS";
+static char __pyx_k_12[] = "id=%s, expected %s parameters, got %s";
+static char __pyx_k_14[] = "Line %s: '%s'\n%s %s: %s\n";
+static char __pyx_k_16[] = "<";
+static char __pyx_k_17[] = "V40_MISSING_ANGLE_BRACKETS";
+static char __pyx_k_18[] = ">";
+static char __pyx_k_19[] = "\"";
+static char __pyx_k_20[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
+static char __pyx_k_21[] = "BADLY_FORMATTED_FORMAT_STRING";
+static char __pyx_k_22[] = "ID=";
+static char __pyx_k_23[] = "Number=";
+static char __pyx_k_24[] = "Type=";
+static char __pyx_k_25[] = "Description=";
+static char __pyx_k_26[] = "FORMAT_MISSING_QUOTES";
+static char __pyx_k_27[] = "<none>";
+static char __pyx_k_28[] = "#alleles";
+static char __pyx_k_29[] = "#nonref_alleles";
+static char __pyx_k_30[] = "#genotypes";
+static char __pyx_k_31[] = "#phased_genotypes";
+static char __pyx_k_33[] = "Unknown number type encountered: %s";
+static char __pyx_k_34[] = "%s=%s";
+static char __pyx_k_35[] = "(Undefined tag)";
+static char __pyx_k_38[] = "(output)";
+static char __pyx_k_39[] = "Genotype Quality";
+static char __pyx_k_40[] = "Read depth at this position for this sample";
+static char __pyx_k_41[] = "Haplotype Quality";
+static char __pyx_k_42[] = "Sample Genotype Filter";
+static char __pyx_k_43[] = "##";
+static char __pyx_k_44[] = "VCFv3.3";
+static char __pyx_k_45[] = "VCFv4.0";
+static char __pyx_k_46[] = "VCFv4.1";
+static char __pyx_k_47[] = "UNKNOWN_FORMAT_STRING";
+static char __pyx_k_48[] = "##fileformat=VCFv%s.%s\n";
+static char __pyx_k_49[] = "##%s=%s\n";
+static char __pyx_k_50[] = "#";
+static char __pyx_k_51[] = "\t";
+static char __pyx_k_52[] = "HEADING_NOT_SEPARATED_BY_TABS";
+static char __pyx_k_53[] = "(%sth entry not found)";
+static char __pyx_k_54[] = "(found %s, expected %s)";
+static char __pyx_k_55[] = "BADLY_FORMATTED_HEADING";
+static char __pyx_k_56[] = "\n";
+static char __pyx_k_57[] = "|";
+static char __pyx_k_58[] = "ERROR_FLAG_HAS_VALUE";
+static char __pyx_k_59[] = "ERROR_FORMAT_NOT_NUMERICAL";
+static char __pyx_k_60[] = "ERROR_FORMAT_NOT_CHAR";
+static char __pyx_k_62[] = "BAD_NUMBER_OF_COLUMNS";
+static char __pyx_k_63[] = "expected %s for %s samples (%s), got %s";
+static char __pyx_k_64[] = "(reference is %s, VCF says %s)";
+static char __pyx_k_65[] = "V33_UNMATCHED_DELETION";
+static char __pyx_k_66[] = "(deletion is %s, reference is %s)";
+static char __pyx_k_67[] = "MISSING_INDEL_ALLELE_REF_BASE";
+static char __pyx_k_68[] = "Required key %s not found in data";
+static char __pyx_k_69[] = "enter_default_format";
+static char __pyx_k_70[] = "Can only handle v3.3 and v4.0 VCF files";
+static char __pyx_k_71[] = "Invalid error string: %s";
+static char __pyx_k_72[] = "needs to be checked";
+static char __pyx_k_73[] = "[|/\\\\]";
+static char __pyx_k_74[] = "^[ACGTN]+$";
+static char __pyx_k_75[] = "id numbertype number type description missingvalue";
+static char __pyx_k_76[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
+static char __pyx_k_77[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
+static char __pyx_k_78[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
+static char __pyx_k_79[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
+static char __pyx_k_80[] = "POS_NOT_NUMERICAL:Position column is not numerical";
+static char __pyx_k_81[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
+static char __pyx_k_82[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
+static char __pyx_k_83[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
+static char __pyx_k_84[] = "POS_NOT_POSITIVE:Position field must be >0";
+static char __pyx_k_85[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
+static char __pyx_k_86[] = "ERROR_INFO_STRING:Error while parsing info field";
+static char __pyx_k_87[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
+static char __pyx_k_88[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
+static char __pyx_k_89[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
+static char __pyx_k_90[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
+static char __pyx_k_91[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
+static char __pyx_k_92[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
+static char __pyx_k_93[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
+static char __pyx_k_94[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
+static char __pyx_k_95[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
+static char __pyx_k_96[] = "MISSING_REF:Reference allele missing";
+static char __pyx_k_97[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
+static char __pyx_k_98[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
+static char __pyx_k_99[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k__0[] = "0";
+static char __pyx_k__D[] = "D";
+static char __pyx_k__I[] = "I";
+static char __pyx_k__N[] = "N";
+static char __pyx_k_100[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
+static char __pyx_k_101[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
+static char __pyx_k_102[] = "WRONG_REF:Wrong reference %s";
+static char __pyx_k_103[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
+static char __pyx_k_104[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
+static char __pyx_k_105[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
+static char __pyx_k_106[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
+static char __pyx_k_107[] = "VCF.getsamples (line 880)";
+static char __pyx_k_108[] = "VCF.setsamples (line 884)";
+static char __pyx_k_109[] = "VCF.getheader (line 888)";
+static char __pyx_k_110[] = "VCF.setheader (line 892)";
+static char __pyx_k_111[] = "VCF.getinfo (line 896)";
+static char __pyx_k_112[] = "VCF.setinfo (line 900)";
+static char __pyx_k_113[] = "VCF.getformat (line 904)";
+static char __pyx_k_114[] = "VCF.setformat (line 908)";
+static char __pyx_k_115[] = "VCF.getfilter (line 912)";
+static char __pyx_k_116[] = "VCF.setfilter (line 916)";
+static char __pyx_k_117[] = "VCF.setreference (line 927)";
+static char __pyx_k_118[] = "VCF.parse (line 939)";
+static char __pyx_k_119[] = "VCF.write (line 946)";
+static char __pyx_k_120[] = "VCF.writeheader (line 952)";
+static char __pyx_k_121[] = "VCF.compare_calls (line 957)";
+static char __pyx_k_122[] = "VCF.connect (line 979)";
+static char __pyx_k_123[] = "VCF.fetch (line 984)";
+static char __pyx_k_124[] = "VCF.validate (line 993)";
+static char __pyx_k__DP[] = "DP";
+static char __pyx_k__FT[] = "FT";
+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__fa[] = "fa";
+static char __pyx_k__id[] = "id";
+static char __pyx_k__re[] = "re";
+static char __pyx_k__ALT[] = "ALT";
+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__fmt[] = "fmt";
+static char __pyx_k__get[] = "get";
+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__opt[] = "opt";
+static char __pyx_k__pos[] = "pos";
+static char __pyx_k__ref[] = "ref";
+static char __pyx_k__sys[] = "sys";
+static char __pyx_k__vcf[] = "vcf";
+static char __pyx_k__zip[] = "zip";
+static char __pyx_k__Flag[] = "Flag";
+static char __pyx_k__INFO[] = "INFO";
+static char __pyx_k__PASS[] = "PASS";
+static char __pyx_k__QUAL[] = "QUAL";
+static char __pyx_k__Type[] = "Type";
+static char __pyx_k__alt1[] = "alt1";
+static char __pyx_k__alt2[] = "alt2";
+static char __pyx_k__copy[] = "copy";
+static char __pyx_k__data[] = "data";
+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__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__self[] = "self";
+static char __pyx_k__type[] = "type";
+static char __pyx_k__ACGTN[] = "ACGTN";
+static char __pyx_k__CHROM[] = "CHROM";
+static char __pyx_k__Error[] = "Error";
+static char __pyx_k__Float[] = "Float";
+static char __pyx_k___copy[] = "_copy";
+static char __pyx_k___info[] = "_info";
+static char __pyx_k___line[] = "_line";
+static char __pyx_k__chrom[] = "chrom";
+static char __pyx_k__descr[] = "descr";
+static char __pyx_k__error[] = "error";
+static char __pyx_k__fetch[] = "fetch";
+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__split[] = "split";
+static char __pyx_k__start[] = "start";
+static char __pyx_k__strip[] = "strip";
+static char __pyx_k__upper[] = "upper";
+static char __pyx_k__value[] = "value";
+static char __pyx_k__write[] = "write";
+static char __pyx_k__FILTER[] = "FILTER";
+static char __pyx_k__FORMAT[] = "FORMAT";
+static char __pyx_k__GTdata[] = "GTdata";
+static char __pyx_k__Number[] = "Number";
+static char __pyx_k__String[] = "String";
+static char __pyx_k___lines[] = "_lines";
+static char __pyx_k___parse[] = "_parse";
+static char __pyx_k__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__parser[] = "parser";
+static char __pyx_k__record[] = "record";
+static char __pyx_k__region[] = "region";
+static char __pyx_k__stderr[] = "stderr";
+static char __pyx_k__stream[] = "stream";
+static char __pyx_k__Integer[] = "Integer";
+static char __pyx_k__Warning[] = "Warning";
+static char __pyx_k____all__[] = "__all__";
+static char __pyx_k___errors[] = "_errors";
+static char __pyx_k___filter[] = "_filter";
+static char __pyx_k___format[] = "_format";
+static char __pyx_k___header[] = "_header";
+static char __pyx_k___lineno[] = "_lineno";
+static char __pyx_k__compile[] = "compile";
+static char __pyx_k__connect[] = "connect";
+static char __pyx_k__getinfo[] = "getinfo";
+static char __pyx_k__missing[] = "missing";
+static char __pyx_k__nfields[] = "nfields";
+static char __pyx_k__regions[] = "regions";
+static char __pyx_k__replace[] = "replace";
+static char __pyx_k__samples[] = "samples";
+static char __pyx_k__setinfo[] = "setinfo";
+static char __pyx_k__vcffile[] = "vcffile";
+static char __pyx_k__version[] = "version";
+static char __pyx_k__GTstring[] = "GTstring";
+static char __pyx_k__Genotype[] = "Genotype";
+static char __pyx_k__KeyError[] = "KeyError";
+static char __pyx_k____dict__[] = "__dict__";
+static char __pyx_k____init__[] = "__init__";
+static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____test__[] = "__test__";
+static char __pyx_k___regions[] = "_regions";
+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__filename[] = "filename";
+static char __pyx_k__gtsRegEx[] = "gtsRegEx";
+static char __pyx_k__inregion[] = "inregion";
+static char __pyx_k__operator[] = "operator";
+static char __pyx_k__validate[] = "validate";
+static char __pyx_k__Character[] = "Character";
+static char __pyx_k__NT_NUMBER[] = "NT_NUMBER";
+static char __pyx_k__Tabixfile[] = "Tabixfile";
+static char __pyx_k__VCFRecord[] = "VCFRecord";
+static char __pyx_k__WRONG_REF[] = "WRONG_REF";
+static char __pyx_k___required[] = "_required";
+static char __pyx_k__convertGT[] = "convertGT";
+static char __pyx_k__enumerate[] = "enumerate";
+static char __pyx_k__getfilter[] = "getfilter";
+static char __pyx_k__getformat[] = "getformat";
+static char __pyx_k__getheader[] = "getheader";
+static char __pyx_k__leftalign[] = "leftalign";
+static char __pyx_k__lineparse[] = "lineparse";
+static char __pyx_k__reference[] = "reference";
+static char __pyx_k__separator[] = "separator";
+static char __pyx_k__setfilter[] = "setfilter";
+static char __pyx_k__setformat[] = "setformat";
+static char __pyx_k__setheader[] = "setheader";
+static char __pyx_k__tabixfile[] = "tabixfile";
+static char __pyx_k__warnerror[] = "warnerror";
+static char __pyx_k__NT_ALLELES[] = "NT_ALLELES";
+static char __pyx_k__NT_UNKNOWN[] = "NT_UNKNOWN";
+static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k___leftalign[] = "_leftalign";
+static char __pyx_k___reference[] = "_reference";
+static char __pyx_k__fileformat[] = "fileformat";
+static char __pyx_k__formatdict[] = "formatdict";
+static char __pyx_k__getsamples[] = "getsamples";
+static char __pyx_k__itemgetter[] = "itemgetter";
+static char __pyx_k__itervalues[] = "itervalues";
+static char __pyx_k__namedtuple[] = "namedtuple";
+static char __pyx_k__numbertype[] = "numbertype";
+static char __pyx_k__parse_data[] = "parse_data";
+static char __pyx_k__setregions[] = "setregions";
+static char __pyx_k__setsamples[] = "setsamples";
+static char __pyx_k__setversion[] = "setversion";
+static char __pyx_k__startswith[] = "startswith";
+static char __pyx_k__write_data[] = "write_data";
+static char __pyx_k__Description[] = "Description";
+static char __pyx_k__MISSING_REF[] = "MISSING_REF";
+static char __pyx_k__V33_BAD_REF[] = "V33_BAD_REF";
+static char __pyx_k__alleleRegEx[] = "alleleRegEx";
+static char __pyx_k__collections[] = "collections";
+static char __pyx_k__defaultdict[] = "defaultdict";
+static char __pyx_k__description[] = "description";
+static char __pyx_k__errorstring[] = "errorstring";
+static char __pyx_k__ignoreerror[] = "ignoreerror";
+static char __pyx_k__writeheader[] = "writeheader";
+static char __pyx_k__BAD_GENOTYPE[] = "BAD_GENOTYPE";
+static char __pyx_k__NT_GENOTYPES[] = "NT_GENOTYPES";
+static char __pyx_k___warn_errors[] = "_warn_errors";
+static char __pyx_k__get_expected[] = "get_expected";
+static char __pyx_k__get_sequence[] = "get_sequence";
+static char __pyx_k__missingvalue[] = "missingvalue";
+static char __pyx_k__parse_format[] = "parse_format";
+static char __pyx_k__parse_header[] = "parse_header";
+static char __pyx_k__setreference[] = "setreference";
+static char __pyx_k__write_header[] = "write_header";
+static char __pyx_k__NT_NR_ALLELES[] = "NT_NR_ALLELES";
+static char __pyx_k__StopIteration[] = "StopIteration";
+static char __pyx_k___parse_header[] = "_parse_header";
+static char __pyx_k__compare_calls[] = "compare_calls";
+static char __pyx_k__convertGTback[] = "convertGTback";
+static char __pyx_k__datagenerator[] = "datagenerator";
+static char __pyx_k__format_format[] = "format_format";
+static char __pyx_k__parse_heading[] = "parse_heading";
+static char __pyx_k__write_heading[] = "write_heading";
+static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
+static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
+static char __pyx_k___sample2column[] = "_sample2column";
+static char __pyx_k___add_definition[] = "_add_definition";
+static char __pyx_k___ignored_errors[] = "_ignored_errors";
+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__ERROR_UNKNOWN_KEY[] = "ERROR_UNKNOWN_KEY";
+static char __pyx_k__POS_NOT_NUMERICAL[] = "POS_NOT_NUMERICAL";
+static char __pyx_k__format_formatdata[] = "format_formatdata";
+static char __pyx_k__FILTER_NOT_DEFINED[] = "FILTER_NOT_DEFINED";
+static char __pyx_k__FORMAT_NOT_DEFINED[] = "FORMAT_NOT_DEFINED";
+static char __pyx_k__QUAL_NOT_NUMERICAL[] = "QUAL_NOT_NUMERICAL";
+static char __pyx_k__ZERO_LENGTH_ALLELE[] = "ZERO_LENGTH_ALLELE";
+static char __pyx_k__ERROR_TRAILING_DATA[] = "ERROR_TRAILING_DATA";
+static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES";
+static char __pyx_k__NotImplementedError[] = "NotImplementedError";
+static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF";
+static PyObject *__pyx_kp_s_1;
+static PyObject *__pyx_kp_s_10;
+static PyObject *__pyx_kp_s_100;
+static PyObject *__pyx_kp_s_101;
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+static PyObject *__pyx_kp_s_88;
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+static PyObject *__pyx_kp_s_93;
+static PyObject *__pyx_kp_s_94;
+static PyObject *__pyx_kp_s_95;
+static PyObject *__pyx_kp_s_96;
+static PyObject *__pyx_kp_s_97;
+static PyObject *__pyx_kp_s_98;
+static PyObject *__pyx_kp_s_99;
+static PyObject *__pyx_kp_s__0;
+static PyObject *__pyx_n_s__ACGTN;
+static PyObject *__pyx_n_s__ALT;
+static PyObject *__pyx_n_s__BAD_GENOTYPE;
+static PyObject *__pyx_n_s__CHROM;
+static PyObject *__pyx_n_s__Character;
+static PyObject *__pyx_n_s__D;
+static PyObject *__pyx_n_s__DP;
+static PyObject *__pyx_n_s__Description;
+static PyObject *__pyx_n_s__ERROR_INFO_STRING;
+static PyObject *__pyx_n_s__ERROR_TRAILING_DATA;
+static PyObject *__pyx_n_s__ERROR_UNKNOWN_KEY;
+static PyObject *__pyx_n_s__Error;
+static PyObject *__pyx_n_s__FILTER;
+static PyObject *__pyx_n_s__FILTER_NOT_DEFINED;
+static PyObject *__pyx_n_s__FORMAT;
+static PyObject *__pyx_n_s__FORMAT_NOT_DEFINED;
+static PyObject *__pyx_n_s__FT;
+static PyObject *__pyx_n_s__Flag;
+static PyObject *__pyx_n_s__Float;
+static PyObject *__pyx_n_s__GQ;
+static PyObject *__pyx_n_s__GT;
+static PyObject *__pyx_n_s__GTdata;
+static PyObject *__pyx_n_s__GTstring;
+static PyObject *__pyx_n_s__Genotype;
+static PyObject *__pyx_n_s__HQ;
+static PyObject *__pyx_n_s__I;
+static PyObject *__pyx_n_s__ID;
+static PyObject *__pyx_n_s__INFO;
+static PyObject *__pyx_n_s__Integer;
+static PyObject *__pyx_n_s__KeyError;
+static PyObject *__pyx_n_s__MISSING_REF;
+static PyObject *__pyx_n_s__N;
+static PyObject *__pyx_n_s__NT_ALLELES;
+static PyObject *__pyx_n_s__NT_GENOTYPES;
+static PyObject *__pyx_n_s__NT_NR_ALLELES;
+static PyObject *__pyx_n_s__NT_NUMBER;
+static PyObject *__pyx_n_s__NT_PHASED_GENOTYPES;
+static PyObject *__pyx_n_s__NT_UNKNOWN;
+static PyObject *__pyx_n_s__NotImplementedError;
+static PyObject *__pyx_n_s__Number;
+static PyObject *__pyx_n_s__PASS;
+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__QUAL;
+static PyObject *__pyx_n_s__QUAL_NOT_NUMERICAL;
+static PyObject *__pyx_n_s__REF;
+static PyObject *__pyx_n_s__StopIteration;
+static PyObject *__pyx_n_s__String;
+static PyObject *__pyx_n_s__Tabixfile;
+static PyObject *__pyx_n_s__Type;
+static PyObject *__pyx_n_s__UNKNOWN_CHAR_IN_REF;
+static PyObject *__pyx_n_s__V33_BAD_ALLELE;
+static PyObject *__pyx_n_s__V33_BAD_REF;
+static PyObject *__pyx_n_s__V40_BAD_ALLELE;
+static PyObject *__pyx_n_s__VCF;
+static PyObject *__pyx_n_s__VCFRecord;
+static PyObject *__pyx_n_s__ValueError;
+static PyObject *__pyx_n_s__WRONG_REF;
+static PyObject *__pyx_n_s__Warning;
+static PyObject *__pyx_n_s__ZERO_LENGTH_ALLELE;
+static PyObject *__pyx_n_s____all__;
+static PyObject *__pyx_n_s____dict__;
+static PyObject *__pyx_n_s____init__;
+static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____test__;
+static PyObject *__pyx_n_s___add_definition;
+static PyObject *__pyx_n_s___copy;
+static PyObject *__pyx_n_s___errors;
+static PyObject *__pyx_n_s___filter;
+static PyObject *__pyx_n_s___format;
+static PyObject *__pyx_n_s___header;
+static PyObject *__pyx_n_s___ignored_errors;
+static PyObject *__pyx_n_s___info;
+static PyObject *__pyx_n_s___leftalign;
+static PyObject *__pyx_n_s___line;
+static PyObject *__pyx_n_s___lineno;
+static PyObject *__pyx_n_s___lines;
+static PyObject *__pyx_n_s___parse;
+static PyObject *__pyx_n_s___parse_header;
+static PyObject *__pyx_n_s___reference;
+static PyObject *__pyx_n_s___regions;
+static PyObject *__pyx_n_s___required;
+static PyObject *__pyx_n_s___sample2column;
+static PyObject *__pyx_n_s___samples;
+static PyObject *__pyx_n_s___version;
+static PyObject *__pyx_n_s___warn_errors;
+static PyObject *__pyx_n_s__add;
+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__bisect;
+static PyObject *__pyx_n_s__buffer;
+static PyObject *__pyx_n_s__chrom;
+static PyObject *__pyx_n_s__collections;
+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__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__end;
+static PyObject *__pyx_n_s__endswith;
+static PyObject *__pyx_n_s__enumerate;
+static PyObject *__pyx_n_s__error;
+static PyObject *__pyx_n_s__errorstring;
+static PyObject *__pyx_n_s__fa;
+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__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__get;
+static PyObject *__pyx_n_s__get_expected;
+static PyObject *__pyx_n_s__get_sequence;
+static PyObject *__pyx_n_s__getfilter;
+static PyObject *__pyx_n_s__getformat;
+static PyObject *__pyx_n_s__getheader;
+static PyObject *__pyx_n_s__getinfo;
+static PyObject *__pyx_n_s__getsamples;
+static PyObject *__pyx_n_s__gtsRegEx;
+static PyObject *__pyx_n_s__header;
+static PyObject *__pyx_n_s__id;
+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__key;
+static PyObject *__pyx_n_s__keys;
+static PyObject *__pyx_n_s__leftalign;
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+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
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+
+static PyObject *__pyx_tp_new_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_4cvcf_VCFRecord *p;
+ PyObject *o = __pyx_ptype_10TabProxies_TupleProxy->tp_new(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_4cvcf_VCFRecord *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_4cvcf_VCFRecord;
+ p->vcf = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pf_4cvcf_9VCFRecord___cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static void __pyx_tp_dealloc_4cvcf_VCFRecord(PyObject *o) {
+ struct __pyx_obj_4cvcf_VCFRecord *p = (struct __pyx_obj_4cvcf_VCFRecord *)o;
+ Py_XDECREF(p->vcf);
+ __pyx_ptype_10TabProxies_TupleProxy->tp_dealloc(o);
+}
+
+static int __pyx_tp_traverse_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_4cvcf_VCFRecord *p = (struct __pyx_obj_4cvcf_VCFRecord *)o;
+ if (__pyx_ptype_10TabProxies_TupleProxy->tp_traverse) {
+ e = __pyx_ptype_10TabProxies_TupleProxy->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->vcf) {
+ e = (*v)(p->vcf, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_4cvcf_VCFRecord(PyObject *o) {
+ struct __pyx_obj_4cvcf_VCFRecord *p = (struct __pyx_obj_4cvcf_VCFRecord *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_10TabProxies_TupleProxy->tp_clear) {
+ __pyx_ptype_10TabProxies_TupleProxy->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->vcf);
+ p->vcf = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *__pyx_sq_item_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) {
+ PyObject *r;
+ PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
+ r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
+ Py_DECREF(x);
+ return r;
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_contig(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_6contig___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_pos(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_3pos___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_id(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_2id___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_ref(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_3ref___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_alt(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_3alt___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_qual(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_4qual___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_filter(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_6filter___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_info(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_4info___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_format(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_6format___get__(o);
+}
+
+static PyObject *__pyx_getprop_4cvcf_9VCFRecord_samples(PyObject *o, void *x) {
+ return __pyx_pf_4cvcf_9VCFRecord_7samples___get__(o);
+}
+
+static PyMethodDef __pyx_methods_4cvcf_VCFRecord[] = {
+ {0, 0, 0, 0}
+};
+
+static struct PyGetSetDef __pyx_getsets_4cvcf_VCFRecord[] = {
+ {(char *)"contig", __pyx_getprop_4cvcf_9VCFRecord_contig, 0, 0, 0},
+ {(char *)"pos", __pyx_getprop_4cvcf_9VCFRecord_pos, 0, 0, 0},
+ {(char *)"id", __pyx_getprop_4cvcf_9VCFRecord_id, 0, 0, 0},
+ {(char *)"ref", __pyx_getprop_4cvcf_9VCFRecord_ref, 0, 0, 0},
+ {(char *)"alt", __pyx_getprop_4cvcf_9VCFRecord_alt, 0, 0, 0},
+ {(char *)"qual", __pyx_getprop_4cvcf_9VCFRecord_qual, 0, 0, 0},
+ {(char *)"filter", __pyx_getprop_4cvcf_9VCFRecord_filter, 0, 0, 0},
+ {(char *)"info", __pyx_getprop_4cvcf_9VCFRecord_info, 0, 0, 0},
+ {(char *)"format", __pyx_getprop_4cvcf_9VCFRecord_format, 0, 0, 0},
+ {(char *)"samples", __pyx_getprop_4cvcf_9VCFRecord_samples, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_VCFRecord = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = {
+ __pyx_pf_4cvcf_9VCFRecord___len__, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ __pyx_sq_item_4cvcf_VCFRecord, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = {
+ __pyx_pf_4cvcf_9VCFRecord___len__, /*mp_length*/
+ __pyx_pf_4cvcf_9VCFRecord___getitem__, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_4cvcf_VCFRecord = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("cvcf.VCFRecord"), /*tp_name*/
+ sizeof(struct __pyx_obj_4cvcf_VCFRecord), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_4cvcf_VCFRecord, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_VCFRecord, /*tp_as_number*/
+ &__pyx_tp_as_sequence_VCFRecord, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_VCFRecord, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_VCFRecord, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("vcf record.\n\n initialized from data and vcf meta \n "), /*tp_doc*/
+ __pyx_tp_traverse_4cvcf_VCFRecord, /*tp_traverse*/
+ __pyx_tp_clear_4cvcf_VCFRecord, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_4cvcf_VCFRecord, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_4cvcf_VCFRecord, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ __pyx_pf_4cvcf_9VCFRecord___init__, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_4cvcf_VCFRecord, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_4cvcf_asVCFRecord *p;
+ PyObject *o = __pyx_ptype_6ctabix_Parser->tp_new(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_4cvcf_asVCFRecord *)o);
+ p->vcffile = Py_None; Py_INCREF(Py_None);
+ return o;
+}
+
+static void __pyx_tp_dealloc_4cvcf_asVCFRecord(PyObject *o) {
+ struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o;
+ Py_XDECREF(p->vcffile);
+ __pyx_ptype_6ctabix_Parser->tp_dealloc(o);
+}
+
+static int __pyx_tp_traverse_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o;
+ if (__pyx_ptype_6ctabix_Parser->tp_traverse) {
+ e = __pyx_ptype_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->vcffile) {
+ e = (*v)(p->vcffile, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_4cvcf_asVCFRecord(PyObject *o) {
+ struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_6ctabix_Parser->tp_clear) {
+ __pyx_ptype_6ctabix_Parser->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->vcffile);
+ p->vcffile = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_4cvcf_asVCFRecord[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_asVCFRecord = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_asVCFRecord = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_asVCFRecord = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("cvcf.asVCFRecord"), /*tp_name*/
+ sizeof(struct __pyx_obj_4cvcf_asVCFRecord), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_4cvcf_asVCFRecord, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_asVCFRecord, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ __pyx_pf_4cvcf_11asVCFRecord___call__, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_asVCFRecord, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/
+ __pyx_tp_traverse_4cvcf_asVCFRecord, /*tp_traverse*/
+ __pyx_tp_clear_4cvcf_asVCFRecord, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_4cvcf_asVCFRecord, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ __pyx_pf_4cvcf_11asVCFRecord___init__, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_4cvcf_asVCFRecord, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyMethodDef __pyx_methods[] = {
+ {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pf_4cvcf_get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("parse_regions"), (PyCFunction)__pyx_pf_4cvcf_parse_regions, METH_O, __Pyx_DOCSTR(0)},
+ {0, 0, 0, 0}
+};
+
+#if PY_MAJOR_VERSION >= 3
+static struct PyModuleDef __pyx_moduledef = {
+ PyModuleDef_HEAD_INIT,
+ __Pyx_NAMESTR("cvcf"),
+ 0, /* m_doc */
+ -1, /* m_size */
+ __pyx_methods /* m_methods */,
+ NULL, /* m_reload */
+ NULL, /* m_traverse */
+ NULL, /* m_clear */
+ NULL /* m_free */
+};
+#endif
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+ __pyx_int_12 = PyInt_FromLong(12); if (unlikely(!__pyx_int_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ __pyx_int_14 = PyInt_FromLong(14); if (unlikely(!__pyx_int_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_17 = PyInt_FromLong(17); if (unlikely(!__pyx_int_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_18 = PyInt_FromLong(18); if (unlikely(!__pyx_int_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__VCF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
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+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__VCF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__connect); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_122), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__VCF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fetch); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_123), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__VCF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__validate); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_124), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "pysam/ctabix.pxd":2
+ *
+ * cdef extern from "string.h": # <<<<<<<<<<<<<<
+ * ctypedef int size_t
+ * void *memcpy(void *dst,void *src,size_t len)
+ */
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
+ if (__pyx_m) {
+ __Pyx_AddTraceback("init cvcf");
+ Py_DECREF(__pyx_m); __pyx_m = 0;
+ } else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_ImportError, "init cvcf");
+ }
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ #if PY_MAJOR_VERSION < 3
+ return;
+ #else
+ return __pyx_m;
+ #endif
+}
+
+/* Runtime support code */
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result)
+ PyErr_SetObject(PyExc_NameError, name);
+ return result;
+}
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
+ #else
+ "%s() got multiple values for keyword argument '%s'", func_name,
+ PyString_AS_STRING(kw_name));
+ #endif
+}
+
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *number, *more_or_less;
+
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ number = (num_expected == 1) ? "" : "s";
+ PyErr_Format(PyExc_TypeError,
+ #if PY_VERSION_HEX < 0x02050000
+ "%s() takes %s %d positional argument%s (%d given)",
+ #else
+ "%s() takes %s %zd positional argument%s (%zd given)",
+ #endif
+ func_name, more_or_less, num_expected, number, num_found);
+}
+
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
+ PyObject *key = 0, *value = 0;
+ Py_ssize_t pos = 0;
+ PyObject*** name;
+ PyObject*** first_kw_arg = argnames + num_pos_args;
+
+ while (PyDict_Next(kwds, &pos, &key, &value)) {
+ name = first_kw_arg;
+ while (*name && (**name != key)) name++;
+ if (*name) {
+ values[name-argnames] = value;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
+ }
+ if (*name) {
+ values[name-argnames] = value;
+ } else {
+ /* unexpected keyword found */
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
+ }
+ }
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
+}
+
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *local_type, *local_value, *local_tb;
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+ if (unlikely(tstate->curexc_type))
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ #endif
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ /* Make sure tstate is in a consistent state when we XDECREF
+ these objects (XDECREF may run arbitrary code). */
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
+
+static double __Pyx__PyObject_AsDouble(PyObject* obj) {
+ PyObject* float_value;
+ if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
+ return PyFloat_AsDouble(obj);
+ } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
+#if PY_MAJOR_VERSION >= 3
+ float_value = PyFloat_FromString(obj);
+#else
+ float_value = PyFloat_FromString(obj, 0);
+#endif
+ } else {
+ PyObject* args = PyTuple_New(1);
+ if (unlikely(!args)) goto bad;
+ PyTuple_SET_ITEM(args, 0, obj);
+ float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
+ PyTuple_SET_ITEM(args, 0, 0);
+ Py_DECREF(args);
+ }
+ if (likely(float_value)) {
+ double value = PyFloat_AS_DOUBLE(float_value);
+ Py_DECREF(float_value);
+ return value;
+ }
+bad:
+ return (double)-1;
+}
+
+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");
+}
+
+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;
+}
+
+static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
+ PyObject *item;
+ if ((item = PyIter_Next(iter))) {
+ Py_DECREF(item);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ }
+ else if (!PyErr_Occurred())
+ return 0;
+ else
+ return -1;
+}
+
+static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
+ Py_ssize_t q = a / b;
+ Py_ssize_t r = a - q*b;
+ q -= ((r != 0) & ((r ^ b) < 0));
+ return q;
+}
+
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->exc_type;
+ *value = tstate->exc_value;
+ *tb = tstate->exc_traceback;
+ Py_XINCREF(*type);
+ Py_XINCREF(*value);
+ Py_XINCREF(*tb);
+}
+
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = type;
+ tstate->exc_value = value;
+ tstate->exc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
+ PyObject *py_import = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
+ if (!py_import)
+ goto bad;
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(py_import);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static PyObject *__Pyx_CreateClass(
+ PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
+{
+ PyObject *py_modname;
+ PyObject *result = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_modname = PyString_FromString(modname);
+ #else
+ py_modname = PyUnicode_FromString(modname);
+ #endif
+ if (!py_modname)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
+ goto bad;
+ #if PY_MAJOR_VERSION < 3
+ result = PyClass_New(bases, dict, name);
+ #else
+ result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
+ #endif
+bad:
+ Py_XDECREF(py_modname);
+ return result;
+}
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ 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;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ 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;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "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 PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ 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
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
+bad:
+ return;
+}
+#endif
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(uint32_t) == sizeof(char)) ||
+ (sizeof(uint32_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(uint32_t) == sizeof(int)) ||
+ (sizeof(uint32_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
+ const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned char" :
+ "value too large to convert to unsigned char");
+ }
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned short" :
+ "value too large to convert to unsigned short");
+ }
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned int" :
+ "value too large to convert to unsigned int");
+ }
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ const char neg_one = (char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to char" :
+ "value too large to convert to char");
+ }
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ const short neg_one = (short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to short" :
+ "value too large to convert to short");
+ }
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ const signed char neg_one = (signed char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed char" :
+ "value too large to convert to signed char");
+ }
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ const signed short neg_one = (signed short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed short" :
+ "value too large to convert to signed short");
+ }
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ const signed int neg_one = (signed int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed int" :
+ "value too large to convert to signed int");
+ }
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+ const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+ const long neg_one = (long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+ const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+ const signed long neg_one = (signed long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return (signed long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+ const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ signed PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+#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)
+{
+ 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
+ if (!py_name)
+ goto bad;
+ result = PyObject_GetAttr(py_module, py_name);
+ Py_DECREF(py_name);
+ py_name = 0;
+ Py_DECREF(py_module);
+ py_module = 0;
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%s.%s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+ if (!strict && ((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);
+ #else
+ PyErr_WarnEx(NULL, warning, 0);
+ #endif
+ }
+ else if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s has the wrong size, try recompiling",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_module);
+ Py_XDECREF(result);
+ return 0;
+}
+#endif
+
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+ PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
+ if (!ob)
+ goto bad;
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+#else
+ *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+#endif
+ if (!*(void **)vtabptr)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+ 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);
+ #else
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (__pyx_clineno) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_code = 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,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ __pyx_lineno, /*int firstlineno,*/
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ if (!py_code) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = __pyx_lineno;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else /* Python 3+ has unicode identifiers */
+ if (t->is_unicode | t->is_str) {
+ if (t->intern) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->encoding) {
+ *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
+ } else {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ }
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ ++t;
+ }
+ return 0;
+}
+
+/* Type Conversion Functions */
+
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ int is_true = x == Py_True;
+ if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
+ else return PyObject_IsTrue(x);
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
+ PyNumberMethods *m;
+ const char *name = NULL;
+ PyObject *res = NULL;
+#if PY_VERSION_HEX < 0x03000000
+ if (PyInt_Check(x) || PyLong_Check(x))
+#else
+ if (PyLong_Check(x))
+#endif
+ return Py_INCREF(x), x;
+ m = Py_TYPE(x)->tp_as_number;
+#if PY_VERSION_HEX < 0x03000000
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Int(x);
+ }
+ else if (m && m->nb_long) {
+ name = "long";
+ res = PyNumber_Long(x);
+ }
+#else
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Long(x);
+ }
+#endif
+ if (res) {
+#if PY_VERSION_HEX < 0x03000000
+ if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+ if (!PyLong_Check(res)) {
+#endif
+ PyErr_Format(PyExc_TypeError,
+ "__%s__ returned non-%s (type %.200s)",
+ name, name, Py_TYPE(res)->tp_name);
+ Py_DECREF(res);
+ return NULL;
+ }
+ }
+ else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_TypeError,
+ "an integer is required");
+ }
+ return res;
+}
+
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject* x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
+}
+
+
+#endif /* Py_PYTHON_H */
projects / pysam.git / blobdiff