-/* Generated by Cython 0.13 on Thu May 5 15:40:49 2011 */
+/* Generated by Cython 0.14.1 on Sat Oct 15 05:27:48 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "bgzf.h"
#include "tabix.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 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 ... */
/* Type declarations */
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
int bedfields;
};
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+/* "cvcf.pyx":94
* ###########################################################################################################
*
* cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/ctabix.pxd":178
+/* "ctabix.pxd":178
* cdef tabix_t * tabixfile
*
* cdef class Parser: # <<<<<<<<<<<<<<
PyObject_HEAD
};
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221
+/* "cvcf.pyx":221
*
*
* cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
PyObject *vcffile;
};
-/* "pysam/ctabix.pxd":172
+/* "ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
};
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+/* "cvcf.pyx":94
* ###########################################################################################################
*
* cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-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 void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_name); /*proto*/
+
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
#define __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;
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 PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*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 PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname); /*proto*/
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+#define __pyx_binding_PyCFunctionType_USED 1
+
+typedef struct {
+ PyCFunctionObject func;
+} __pyx_binding_PyCFunctionType_object;
+
+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
+#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
+
+static int __pyx_binding_PyCFunctionType_init(void); /* proto */
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
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;
+static int __pyx_module_is_main_cvcf = 0;
/* Implementation of cvcf */
static PyObject *__pyx_builtin_object;
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_4[] = ":";
+static char __pyx_k_6[] = "-";
+static char __pyx_k_8[] = "Don't understand region string '%s'";
+static char __pyx_k_9[] = ".";
+static char __pyx_k_11[] = ";";
+static char __pyx_k_14[] = "=";
+static char __pyx_k_18[] = "BAD_NUMBER_OF_VALUES";
+static char __pyx_k_19[] = "(found %s values in element %s; expected %s)";
+static char __pyx_k_20[] = "BAD_NUMBER_OF_PARAMETERS";
+static char __pyx_k_21[] = "id=%s, expected %s parameters, got %s";
+static char __pyx_k_25[] = "Line %s: '%s'\n%s %s: %s\n";
+static char __pyx_k_27[] = "<";
+static char __pyx_k_29[] = "V40_MISSING_ANGLE_BRACKETS";
+static char __pyx_k_30[] = ">";
+static char __pyx_k_34[] = "\"";
+static char __pyx_k_38[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
+static char __pyx_k_39[] = "BADLY_FORMATTED_FORMAT_STRING";
+static char __pyx_k_40[] = "ID=";
+static char __pyx_k_41[] = "Number=";
+static char __pyx_k_42[] = "Type=";
+static char __pyx_k_43[] = "Description=";
+static char __pyx_k_52[] = "FORMAT_MISSING_QUOTES";
+static char __pyx_k_55[] = "<none>";
+static char __pyx_k_56[] = "#alleles";
+static char __pyx_k_57[] = "#nonref_alleles";
+static char __pyx_k_58[] = "#genotypes";
+static char __pyx_k_59[] = "#phased_genotypes";
+static char __pyx_k_61[] = "Unknown number type encountered: %s";
+static char __pyx_k_62[] = "%s=%s";
+static char __pyx_k_63[] = "(Undefined tag)";
+static char __pyx_k_66[] = "(output)";
+static char __pyx_k_69[] = "Genotype Quality";
+static char __pyx_k_70[] = "Read depth at this position for this sample";
+static char __pyx_k_71[] = "Haplotype Quality";
+static char __pyx_k_72[] = "Sample Genotype Filter";
+static char __pyx_k_73[] = "##";
+static char __pyx_k_76[] = "VCFv3.3";
+static char __pyx_k_77[] = "VCFv4.0";
+static char __pyx_k_78[] = "VCFv4.1";
+static char __pyx_k_79[] = "UNKNOWN_FORMAT_STRING";
+static char __pyx_k_80[] = "##fileformat=VCFv%s.%s\n";
+static char __pyx_k_81[] = "##%s=%s\n";
+static char __pyx_k_82[] = "#";
+static char __pyx_k_85[] = "\t";
+static char __pyx_k_87[] = "HEADING_NOT_SEPARATED_BY_TABS";
+static char __pyx_k_88[] = "(%sth entry not found)";
+static char __pyx_k_89[] = "(found %s, expected %s)";
+static char __pyx_k_90[] = "BADLY_FORMATTED_HEADING";
+static char __pyx_k_91[] = "\n";
+static char __pyx_k_92[] = "|";
+static char __pyx_k_93[] = "ERROR_FLAG_HAS_VALUE";
+static char __pyx_k_97[] = "ERROR_FORMAT_NOT_NUMERICAL";
+static char __pyx_k_98[] = "ERROR_FORMAT_NOT_CHAR";
static char __pyx_k__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_101[] = "BAD_NUMBER_OF_COLUMNS";
+static char __pyx_k_102[] = "expected %s for %s samples (%s), got %s";
+static char __pyx_k_103[] = "(reference is %s, VCF says %s)";
+static char __pyx_k_111[] = "V33_UNMATCHED_DELETION";
+static char __pyx_k_112[] = "(deletion is %s, reference is %s)";
+static char __pyx_k_113[] = "MISSING_INDEL_ALLELE_REF_BASE";
+static char __pyx_k_115[] = "Required key %s not found in data";
+static char __pyx_k_118[] = "enter_default_format";
+static char __pyx_k_119[] = "Can only handle v3.3 and v4.0 VCF files";
+static char __pyx_k_121[] = "Invalid error string: %s";
+static char __pyx_k_122[] = "needs to be checked";
+static char __pyx_k_126[] = "[|/\\\\]";
+static char __pyx_k_128[] = "^[ACGTN]+$";
+static char __pyx_k_130[] = "id numbertype number type description missingvalue";
+static char __pyx_k_132[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
+static char __pyx_k_133[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
+static char __pyx_k_134[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
+static char __pyx_k_135[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
+static char __pyx_k_136[] = "POS_NOT_NUMERICAL:Position column is not numerical";
+static char __pyx_k_137[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
+static char __pyx_k_138[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
+static char __pyx_k_139[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
+static char __pyx_k_140[] = "POS_NOT_POSITIVE:Position field must be >0";
+static char __pyx_k_141[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
+static char __pyx_k_142[] = "ERROR_INFO_STRING:Error while parsing info field";
+static char __pyx_k_143[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
+static char __pyx_k_144[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
+static char __pyx_k_145[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
+static char __pyx_k_146[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
+static char __pyx_k_147[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
+static char __pyx_k_148[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
+static char __pyx_k_149[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
+static char __pyx_k_150[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
+static char __pyx_k_151[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
+static char __pyx_k_152[] = "MISSING_REF:Reference allele missing";
+static char __pyx_k_153[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
+static char __pyx_k_154[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
+static char __pyx_k_155[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k_156[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
+static char __pyx_k_157[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
+static char __pyx_k_158[] = "WRONG_REF:Wrong reference %s";
+static char __pyx_k_159[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
+static char __pyx_k_160[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
+static char __pyx_k_161[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
+static char __pyx_k_162[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
static char __pyx_k__DP[] = "DP";
static char __pyx_k__FT[] = "FT";
static char __pyx_k__GQ[] = "GQ";
static char __pyx_k__alt1[] = "alt1";
static char __pyx_k__alt2[] = "alt2";
static char __pyx_k__copy[] = "copy";
+static char __pyx_k__cvcf[] = "cvcf";
static char __pyx_k__data[] = "data";
static char __pyx_k__find[] = "find";
static char __pyx_k__info[] = "info";
static char __pyx_k__String[] = "String";
static char __pyx_k___lines[] = "_lines";
static char __pyx_k___parse[] = "_parse";
+static char __pyx_k__append[] = "append";
static char __pyx_k__bisect[] = "bisect";
static char __pyx_k__buffer[] = "buffer";
static char __pyx_k__contig[] = "contig";
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__parse_regions[] = "parse_regions";
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__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;
+static PyObject *__pyx_n_s_101;
static PyObject *__pyx_kp_s_102;
static PyObject *__pyx_kp_s_103;
-static PyObject *__pyx_kp_s_104;
-static PyObject *__pyx_kp_s_105;
-static PyObject *__pyx_kp_s_106;
-static PyObject *__pyx_kp_u_107;
-static PyObject *__pyx_kp_u_108;
-static PyObject *__pyx_kp_u_109;
-static PyObject *__pyx_n_s_11;
-static PyObject *__pyx_kp_u_110;
-static PyObject *__pyx_kp_u_111;
-static PyObject *__pyx_kp_u_112;
-static PyObject *__pyx_kp_u_113;
-static PyObject *__pyx_kp_u_114;
-static PyObject *__pyx_kp_u_115;
-static PyObject *__pyx_kp_u_116;
-static PyObject *__pyx_kp_u_117;
-static PyObject *__pyx_kp_u_118;
-static PyObject *__pyx_kp_u_119;
-static PyObject *__pyx_kp_s_12;
-static PyObject *__pyx_kp_u_120;
-static PyObject *__pyx_kp_u_121;
-static PyObject *__pyx_kp_u_122;
-static PyObject *__pyx_kp_u_123;
-static PyObject *__pyx_kp_u_124;
+static PyObject *__pyx_kp_s_11;
+static PyObject *__pyx_n_s_111;
+static PyObject *__pyx_kp_s_112;
+static PyObject *__pyx_n_s_113;
+static PyObject *__pyx_kp_s_115;
+static PyObject *__pyx_n_s_118;
+static PyObject *__pyx_kp_s_119;
+static PyObject *__pyx_kp_s_121;
+static PyObject *__pyx_kp_s_122;
+static PyObject *__pyx_kp_s_126;
+static PyObject *__pyx_kp_s_128;
+static PyObject *__pyx_kp_s_130;
+static PyObject *__pyx_kp_s_132;
+static PyObject *__pyx_kp_s_133;
+static PyObject *__pyx_kp_s_134;
+static PyObject *__pyx_kp_s_135;
+static PyObject *__pyx_kp_s_136;
+static PyObject *__pyx_kp_s_137;
+static PyObject *__pyx_kp_s_138;
+static PyObject *__pyx_kp_s_139;
static PyObject *__pyx_kp_s_14;
-static PyObject *__pyx_kp_s_16;
-static PyObject *__pyx_n_s_17;
-static PyObject *__pyx_kp_s_18;
+static PyObject *__pyx_kp_s_140;
+static PyObject *__pyx_kp_s_141;
+static PyObject *__pyx_kp_s_142;
+static PyObject *__pyx_kp_s_143;
+static PyObject *__pyx_kp_s_144;
+static PyObject *__pyx_kp_s_145;
+static PyObject *__pyx_kp_s_146;
+static PyObject *__pyx_kp_s_147;
+static PyObject *__pyx_kp_s_148;
+static PyObject *__pyx_kp_s_149;
+static PyObject *__pyx_kp_s_150;
+static PyObject *__pyx_kp_s_151;
+static PyObject *__pyx_kp_s_152;
+static PyObject *__pyx_kp_s_153;
+static PyObject *__pyx_kp_s_154;
+static PyObject *__pyx_kp_s_155;
+static PyObject *__pyx_kp_s_156;
+static PyObject *__pyx_kp_s_157;
+static PyObject *__pyx_kp_s_158;
+static PyObject *__pyx_kp_s_159;
+static PyObject *__pyx_kp_s_160;
+static PyObject *__pyx_kp_s_161;
+static PyObject *__pyx_kp_s_162;
+static PyObject *__pyx_n_s_18;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_n_s_20;
-static PyObject *__pyx_n_s_21;
-static PyObject *__pyx_kp_s_22;
-static PyObject *__pyx_kp_s_23;
-static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_kp_s_21;
static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_n_s_26;
static PyObject *__pyx_kp_s_27;
-static PyObject *__pyx_kp_s_28;
-static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_3;
+static PyObject *__pyx_n_s_29;
static PyObject *__pyx_kp_s_30;
-static PyObject *__pyx_kp_s_31;
-static PyObject *__pyx_kp_s_33;
static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_35;
-static PyObject *__pyx_kp_s_38;
-static PyObject *__pyx_kp_s_39;
+static PyObject *__pyx_n_s_38;
+static PyObject *__pyx_n_s_39;
static PyObject *__pyx_kp_s_4;
static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_41;
static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
-static PyObject *__pyx_kp_s_44;
-static PyObject *__pyx_kp_s_45;
-static PyObject *__pyx_kp_s_46;
-static PyObject *__pyx_n_s_47;
-static PyObject *__pyx_kp_s_48;
-static PyObject *__pyx_kp_s_49;
-static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_50;
-static PyObject *__pyx_kp_s_51;
static PyObject *__pyx_n_s_52;
-static PyObject *__pyx_kp_s_53;
-static PyObject *__pyx_kp_s_54;
-static PyObject *__pyx_n_s_55;
+static PyObject *__pyx_kp_s_55;
static PyObject *__pyx_kp_s_56;
static PyObject *__pyx_kp_s_57;
-static PyObject *__pyx_n_s_58;
-static PyObject *__pyx_n_s_59;
-static PyObject *__pyx_kp_b_6;
+static PyObject *__pyx_kp_s_58;
+static PyObject *__pyx_kp_s_59;
static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_n_s_60;
-static PyObject *__pyx_n_s_62;
+static PyObject *__pyx_kp_s_61;
+static PyObject *__pyx_kp_s_62;
static PyObject *__pyx_kp_s_63;
-static PyObject *__pyx_kp_s_64;
-static PyObject *__pyx_n_s_65;
static PyObject *__pyx_kp_s_66;
-static PyObject *__pyx_n_s_67;
-static PyObject *__pyx_kp_s_68;
-static PyObject *__pyx_n_s_69;
-static PyObject *__pyx_kp_s_7;
+static PyObject *__pyx_kp_s_69;
static PyObject *__pyx_kp_s_70;
static PyObject *__pyx_kp_s_71;
static PyObject *__pyx_kp_s_72;
static PyObject *__pyx_kp_s_73;
-static PyObject *__pyx_kp_s_74;
-static PyObject *__pyx_kp_s_75;
static PyObject *__pyx_kp_s_76;
static PyObject *__pyx_kp_s_77;
static PyObject *__pyx_kp_s_78;
-static PyObject *__pyx_kp_s_79;
+static PyObject *__pyx_n_s_79;
static PyObject *__pyx_kp_s_8;
static PyObject *__pyx_kp_s_80;
static PyObject *__pyx_kp_s_81;
static PyObject *__pyx_kp_s_82;
-static PyObject *__pyx_kp_s_83;
-static PyObject *__pyx_kp_s_84;
static PyObject *__pyx_kp_s_85;
-static PyObject *__pyx_kp_s_86;
-static PyObject *__pyx_kp_s_87;
+static PyObject *__pyx_n_s_87;
static PyObject *__pyx_kp_s_88;
static PyObject *__pyx_kp_s_89;
-static PyObject *__pyx_n_s_9;
-static PyObject *__pyx_kp_s_90;
+static PyObject *__pyx_kp_b_9;
+static PyObject *__pyx_kp_s_9;
+static PyObject *__pyx_n_s_90;
static PyObject *__pyx_kp_s_91;
static PyObject *__pyx_kp_s_92;
-static PyObject *__pyx_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_n_s_93;
+static PyObject *__pyx_n_s_97;
+static PyObject *__pyx_n_s_98;
+static PyObject *__pyx_kp_b__0;
static PyObject *__pyx_kp_s__0;
static PyObject *__pyx_n_s__ACGTN;
static PyObject *__pyx_n_s__ALT;
static PyObject *__pyx_n_s__NT_UNKNOWN;
static PyObject *__pyx_n_s__NotImplementedError;
static PyObject *__pyx_n_s__Number;
+static PyObject *__pyx_n_b__PASS;
static PyObject *__pyx_n_s__PASS;
static PyObject *__pyx_n_s__POS;
static PyObject *__pyx_n_s__POS_NOT_NUMERICAL;
static PyObject *__pyx_n_s__alt;
static PyObject *__pyx_n_s__alt1;
static PyObject *__pyx_n_s__alt2;
+static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__bisect;
static PyObject *__pyx_n_s__buffer;
static PyObject *__pyx_n_s__chrom;
static PyObject *__pyx_n_s__convertGT;
static PyObject *__pyx_n_s__convertGTback;
static PyObject *__pyx_n_s__copy;
+static PyObject *__pyx_n_s__cvcf;
static PyObject *__pyx_n_s__data;
static PyObject *__pyx_n_s__datagenerator;
static PyObject *__pyx_n_s__deepcopy;
static PyObject *__pyx_n_s__parse_formatdata;
static PyObject *__pyx_n_s__parse_header;
static PyObject *__pyx_n_s__parse_heading;
+static PyObject *__pyx_n_s__parse_regions;
static PyObject *__pyx_n_s__parser;
static PyObject *__pyx_n_s__pos;
static PyObject *__pyx_n_s__pos1;
static PyObject *__pyx_int_40;
static PyObject *__pyx_int_100;
static PyObject *__pyx_int_3000000000;
-static PyObject *__pyx_k_13;
-static PyObject *__pyx_k_15;
-static PyObject *__pyx_k_32;
-static PyObject *__pyx_k_36;
-static PyObject *__pyx_k_37;
-static PyObject *__pyx_k_61;
-
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":58
+static PyObject *__pyx_k_22;
+static PyObject *__pyx_k_26;
+static PyObject *__pyx_k_60;
+static PyObject *__pyx_k_64;
+static PyObject *__pyx_k_65;
+static PyObject *__pyx_k_99;
+static PyObject *__pyx_k_tuple_3;
+static PyObject *__pyx_k_tuple_5;
+static PyObject *__pyx_k_tuple_7;
+static PyObject *__pyx_k_tuple_10;
+static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_13;
+static PyObject *__pyx_k_tuple_15;
+static PyObject *__pyx_k_tuple_16;
+static PyObject *__pyx_k_tuple_17;
+static PyObject *__pyx_k_tuple_23;
+static PyObject *__pyx_k_tuple_24;
+static PyObject *__pyx_k_tuple_28;
+static PyObject *__pyx_k_tuple_31;
+static PyObject *__pyx_k_tuple_32;
+static PyObject *__pyx_k_tuple_33;
+static PyObject *__pyx_k_tuple_35;
+static PyObject *__pyx_k_tuple_36;
+static PyObject *__pyx_k_tuple_37;
+static PyObject *__pyx_k_tuple_44;
+static PyObject *__pyx_k_tuple_45;
+static PyObject *__pyx_k_tuple_46;
+static PyObject *__pyx_k_tuple_47;
+static PyObject *__pyx_k_tuple_48;
+static PyObject *__pyx_k_tuple_49;
+static PyObject *__pyx_k_tuple_50;
+static PyObject *__pyx_k_tuple_51;
+static PyObject *__pyx_k_tuple_53;
+static PyObject *__pyx_k_tuple_54;
+static PyObject *__pyx_k_tuple_67;
+static PyObject *__pyx_k_tuple_68;
+static PyObject *__pyx_k_tuple_74;
+static PyObject *__pyx_k_tuple_75;
+static PyObject *__pyx_k_tuple_83;
+static PyObject *__pyx_k_tuple_84;
+static PyObject *__pyx_k_tuple_86;
+static PyObject *__pyx_k_tuple_94;
+static PyObject *__pyx_k_tuple_95;
+static PyObject *__pyx_k_tuple_96;
+static PyObject *__pyx_k_tuple_100;
+static PyObject *__pyx_k_tuple_104;
+static PyObject *__pyx_k_tuple_105;
+static PyObject *__pyx_k_tuple_106;
+static PyObject *__pyx_k_tuple_107;
+static PyObject *__pyx_k_tuple_108;
+static PyObject *__pyx_k_tuple_109;
+static PyObject *__pyx_k_tuple_110;
+static PyObject *__pyx_k_tuple_114;
+static PyObject *__pyx_k_tuple_116;
+static PyObject *__pyx_k_tuple_117;
+static PyObject *__pyx_k_tuple_120;
+static PyObject *__pyx_k_tuple_123;
+static PyObject *__pyx_k_tuple_124;
+static PyObject *__pyx_k_tuple_125;
+static PyObject *__pyx_k_tuple_127;
+static PyObject *__pyx_k_tuple_129;
+static PyObject *__pyx_k_tuple_131;
+
+/* "cvcf.pyx":58
*
* # Utility function. Uses 0-based coordinates
* def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
*/
static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pf_4cvcf_get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_chrom = 0;
PyObject *__pyx_v_start = 0;
__pyx_L4_argument_unpacking_done:;
__pyx_v_sequence = Py_None; __Pyx_INCREF(Py_None);
- /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":60
+ /* "cvcf.pyx":60
* def get_sequence(chrom, start, end, fa):
* # obtain sequence from .fa file, without truncation
* if end<=start: return "" # <<<<<<<<<<<<<<
}
__pyx_L6:;
- /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":61
+ /* "cvcf.pyx":61
* # obtain sequence from .fa file, without truncation
* if end<=start: return ""
* if not fa: return "N"*(end-start) # <<<<<<<<<<<<<<
}
__pyx_L7:;
- /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":62
+ /* "cvcf.pyx":62
* if end<=start: return ""
* if not fa: return "N"*(end-start)
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() # <<<<<<<<<<<<<<
__pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
__Pyx_INCREF(__pyx_v_fa);
PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_v_fa);
__Pyx_GIVEREF(__pyx_v_fa);
- __pyx_t_6 = PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
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{&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0},
{&__pyx_kp_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 0},
{&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0},
{&__pyx_kp_s_82, __pyx_k_82, sizeof(__pyx_k_82), 0, 0, 1, 0},
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{&__pyx_kp_s_88, __pyx_k_88, sizeof(__pyx_k_88), 0, 0, 1, 0},
{&__pyx_kp_s_89, __pyx_k_89, sizeof(__pyx_k_89), 0, 0, 1, 0},
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{&__pyx_kp_s_91, __pyx_k_91, sizeof(__pyx_k_91), 0, 0, 1, 0},
{&__pyx_kp_s_92, __pyx_k_92, sizeof(__pyx_k_92), 0, 0, 1, 0},
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{&__pyx_kp_s__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 1, 0},
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{&__pyx_n_s__Number, __pyx_k__Number, sizeof(__pyx_k__Number), 0, 0, 1, 1},
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{&__pyx_n_s__alt2, __pyx_k__alt2, sizeof(__pyx_k__alt2), 0, 0, 1, 1},
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{&__pyx_n_s__bisect, __pyx_k__bisect, sizeof(__pyx_k__bisect), 0, 0, 1, 1},
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{&__pyx_n_s__copy, __pyx_k__copy, sizeof(__pyx_k__copy), 0, 0, 1, 1},
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{&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1},
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{&__pyx_n_s__parse_heading, __pyx_k__parse_heading, sizeof(__pyx_k__parse_heading), 0, 0, 1, 1},
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{&__pyx_n_s__parser, __pyx_k__parser, sizeof(__pyx_k__parser), 0, 0, 1, 1},
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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;};
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- __pyx_int_33 = PyInt_FromLong(33); if (unlikely(!__pyx_int_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+{
+ 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 int __Pyx_ParseOptionalKeywords(
PyObject *kwds,
PyObject **argnames[],
}
-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))
+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 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 PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ }
+ 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;
- #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;
+ }
+
+ 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:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
+ return;
}
-
+#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
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 PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
+ PyObject *metaclass;
+ /* Default metaclass */
+#if PY_MAJOR_VERSION < 3
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = PyObject_GetAttrString(base, "__class__");
+ if (!metaclass) {
+ PyErr_Clear();
+ metaclass = (PyObject*) Py_TYPE(base);
+ }
+ } else {
+ metaclass = (PyObject *) &PyClass_Type;
+ }
+#else
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = (PyObject*) Py_TYPE(base);
+ } else {
+ metaclass = (PyObject *) &PyType_Type;
+ }
+#endif
+ Py_INCREF(metaclass);
+ return metaclass;
}
-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;
-}
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname) {
+ PyObject *result;
+ PyObject *metaclass;
+ if (PyDict_SetItemString(dict, "__module__", modname) < 0)
+ return NULL;
-#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
+ /* Python2 __metaclass__ */
+ metaclass = PyDict_GetItemString(dict, "__metaclass__");
+ if (metaclass) {
+ Py_INCREF(metaclass);
+ } else {
+ metaclass = __Pyx_FindPy2Metaclass(bases);
}
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
+ result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
+ Py_DECREF(metaclass);
+ return result;
}
-#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;
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
+ __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
+ if (op == NULL)
+ return NULL;
+ op->func.m_ml = ml;
+ Py_XINCREF(self);
+ op->func.m_self = self;
+ Py_XINCREF(module);
+ op->func.m_module = module;
+ PyObject_GC_Track(op);
+ return (PyObject *)op;
+}
- 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;
- }
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
+ PyObject_GC_UnTrack(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
+ PyObject_GC_Del(m);
+}
- PyErr_SetObject(type, value);
+static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
+ if (obj == Py_None)
+ obj = NULL;
+ return PyMethod_New(func, obj, type);
+}
- 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);
- }
+static int __pyx_binding_PyCFunctionType_init(void) {
+ __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
+ __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
+ __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
+ __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
+ if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
+ return -1;
}
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
+ return 0;
-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;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ 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),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
#endif
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+static void* __Pyx_GetVtable(PyObject *dict) {
+ void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
if (!ob)
goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+ ptr = PyCapsule_GetPointer(ob, 0);
#else
- *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+ ptr = PyCObject_AsVoidPtr(ob);
#endif
- if (!*(void **)vtabptr)
- goto bad;
+ if (!ptr && !PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
Py_DECREF(ob);
- return 0;
+ return ptr;
bad:
Py_XDECREF(ob);
- return -1;
+ return NULL;
}
static int __Pyx_SetVtable(PyObject *dict, void *vtable) {