X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fcvcf.c;h=82eae7d1868ff4b1072995053ff6b22929a2d1c7;hp=d194519d5e20e227a6c1d69ba9d9128e3f26b897;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109 diff --git a/pysam/cvcf.c b/pysam/cvcf.c index d194519..82eae7d 100644 --- a/pysam/cvcf.c +++ b/pysam/cvcf.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.14.1 on Sat Oct 15 05:27:48 2011 */ +/* Generated by Cython 0.13 on Thu May 5 15:40:49 2011 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -126,20 +126,15 @@ #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) @@ -156,7 +151,7 @@ #endif #if PY_MAJOR_VERSION >= 3 - #define PyBoolObject PyLongObject + #define PyBoolObject PyLongObject #endif @@ -168,25 +163,6 @@ #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 @@ -232,11 +208,6 @@ #include "bgzf.h" #include "tabix.h" -#ifdef PYREX_WITHOUT_ASSERTIONS -#define CYTHON_WITHOUT_ASSERTIONS -#endif - - /* inline attribute */ #ifndef CYTHON_INLINE #if defined(__GNUC__) @@ -246,7 +217,7 @@ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else - #define CYTHON_INLINE + #define CYTHON_INLINE #endif #endif @@ -254,14 +225,14 @@ #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 @@ -286,7 +257,7 @@ static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #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 ... */ @@ -316,7 +287,7 @@ static const char *__pyx_f[] = { /* Type declarations */ -/* "TabProxies.pxd":42 +/* "pysam/TabProxies.pxd":42 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< @@ -336,7 +307,7 @@ struct __pyx_obj_10TabProxies_TupleProxy { int is_modified; }; -/* "TabProxies.pxd":77 +/* "pysam/TabProxies.pxd":77 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< @@ -348,7 +319,7 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy { struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; }; -/* "TabProxies.pxd":80 +/* "pysam/TabProxies.pxd":80 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -364,7 +335,7 @@ struct __pyx_obj_10TabProxies_BedProxy { int bedfields; }; -/* "cvcf.pyx":94 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94 * ########################################################################################################### * * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< @@ -379,7 +350,7 @@ struct __pyx_obj_4cvcf_VCFRecord { uint32_t pos; }; -/* "TabProxies.pxd":91 +/* "pysam/TabProxies.pxd":91 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -393,7 +364,7 @@ struct __pyx_obj_10TabProxies_VCFProxy { uint32_t pos; }; -/* "ctabix.pxd":178 +/* "pysam/ctabix.pxd":178 * cdef tabix_t * tabixfile * * cdef class Parser: # <<<<<<<<<<<<<< @@ -404,7 +375,7 @@ struct __pyx_obj_6ctabix_Parser { PyObject_HEAD }; -/* "TabProxies.pxd":60 +/* "pysam/TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< @@ -426,7 +397,7 @@ struct __pyx_obj_10TabProxies_GTFProxy { int hasOwnAttributes; }; -/* "cvcf.pyx":221 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221 * * * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<< @@ -439,7 +410,7 @@ struct __pyx_obj_4cvcf_asVCFRecord { PyObject *vcffile; }; -/* "ctabix.pxd":172 +/* "pysam/ctabix.pxd":172 * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) * * cdef class Tabixfile: # <<<<<<<<<<<<<< @@ -454,7 +425,7 @@ struct __pyx_obj_6ctabix_Tabixfile { }; -/* "TabProxies.pxd":42 +/* "pysam/TabProxies.pxd":42 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< @@ -472,7 +443,7 @@ struct __pyx_vtabstruct_10TabProxies_TupleProxy { static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy; -/* "TabProxies.pxd":77 +/* "pysam/TabProxies.pxd":77 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< @@ -486,7 +457,7 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy { static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy; -/* "TabProxies.pxd":91 +/* "pysam/TabProxies.pxd":91 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -500,7 +471,7 @@ struct __pyx_vtabstruct_10TabProxies_VCFProxy { static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy; -/* "TabProxies.pxd":60 +/* "pysam/TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< @@ -514,7 +485,7 @@ struct __pyx_vtabstruct_10TabProxies_GTFProxy { static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy; -/* "cvcf.pyx":94 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94 * ########################################################################################################### * * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< @@ -528,7 +499,7 @@ struct __pyx_vtabstruct_4cvcf_VCFRecord { static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord; -/* "TabProxies.pxd":80 +/* "pysam/TabProxies.pxd":80 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -589,12 +560,12 @@ static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ -static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, - Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ - static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name); /*proto*/ +static 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*/ @@ -673,11 +644,6 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ - -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ - static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ #define __Pyx_PyObject_AsDouble(obj) \ @@ -686,6 +652,7 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void); + #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; @@ -856,24 +823,12 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/ -static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ - -static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, - PyObject *modname); /*proto*/ +static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*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 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 int __pyx_binding_PyCFunctionType_init(void); /* proto */ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); @@ -913,7 +868,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ -static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ +static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ @@ -936,7 +891,7 @@ static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0; static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0; static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0; #define __Pyx_MODULE_NAME "cvcf" -static int __pyx_module_is_main_cvcf = 0; +int __pyx_module_is_main_cvcf = 0; /* Implementation of cvcf */ static PyObject *__pyx_builtin_object; @@ -952,108 +907,126 @@ static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_NotImplementedError; static char __pyx_k_1[] = ""; static char __pyx_k_2[] = ","; -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[] = ""; -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_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[] = ""; +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_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_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"; @@ -1090,7 +1063,6 @@ 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__cvcf[] = "cvcf"; static char __pyx_k__data[] = "data"; static char __pyx_k__find[] = "find"; static char __pyx_k__info[] = "info"; @@ -1133,7 +1105,6 @@ static char __pyx_k__Number[] = "Number"; static char __pyx_k__String[] = "String"; static char __pyx_k___lines[] = "_lines"; static char __pyx_k___parse[] = "_parse"; -static char __pyx_k__append[] = "append"; static char __pyx_k__bisect[] = "bisect"; static char __pyx_k__buffer[] = "buffer"; static char __pyx_k__contig[] = "contig"; @@ -1251,7 +1222,6 @@ 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__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"; @@ -1273,107 +1243,124 @@ static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF"; static PyObject *__pyx_kp_s_1; -static PyObject *__pyx_n_s_101; +static PyObject *__pyx_kp_s_10; +static PyObject *__pyx_kp_s_100; +static PyObject *__pyx_kp_s_101; static PyObject *__pyx_kp_s_102; static PyObject *__pyx_kp_s_103; -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_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_14; -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_16; +static PyObject *__pyx_n_s_17; +static PyObject *__pyx_kp_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_2; static PyObject *__pyx_n_s_20; -static PyObject *__pyx_kp_s_21; +static PyObject *__pyx_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_25; +static PyObject *__pyx_n_s_26; static PyObject *__pyx_kp_s_27; -static PyObject *__pyx_n_s_29; +static PyObject *__pyx_kp_s_28; +static PyObject *__pyx_kp_s_29; +static PyObject *__pyx_kp_s_3; 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_n_s_38; -static PyObject *__pyx_n_s_39; +static PyObject *__pyx_kp_s_35; +static PyObject *__pyx_kp_s_38; +static PyObject *__pyx_kp_s_39; static PyObject *__pyx_kp_s_4; static PyObject *__pyx_kp_s_40; static PyObject *__pyx_kp_s_41; static PyObject *__pyx_kp_s_42; static PyObject *__pyx_kp_s_43; +static PyObject *__pyx_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_55; +static PyObject *__pyx_kp_s_53; +static PyObject *__pyx_kp_s_54; +static PyObject *__pyx_n_s_55; static PyObject *__pyx_kp_s_56; static PyObject *__pyx_kp_s_57; -static PyObject *__pyx_kp_s_58; -static PyObject *__pyx_kp_s_59; +static PyObject *__pyx_n_s_58; +static PyObject *__pyx_n_s_59; +static PyObject *__pyx_kp_b_6; static PyObject *__pyx_kp_s_6; -static PyObject *__pyx_kp_s_61; -static PyObject *__pyx_kp_s_62; +static PyObject *__pyx_n_s_60; +static PyObject *__pyx_n_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_kp_s_69; +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_70; static PyObject *__pyx_kp_s_71; static PyObject *__pyx_kp_s_72; static PyObject *__pyx_kp_s_73; +static PyObject *__pyx_kp_s_74; +static PyObject *__pyx_kp_s_75; static PyObject *__pyx_kp_s_76; static PyObject *__pyx_kp_s_77; static PyObject *__pyx_kp_s_78; -static PyObject *__pyx_n_s_79; +static PyObject *__pyx_kp_s_79; static PyObject *__pyx_kp_s_8; static PyObject *__pyx_kp_s_80; static PyObject *__pyx_kp_s_81; static PyObject *__pyx_kp_s_82; +static PyObject *__pyx_kp_s_83; +static PyObject *__pyx_kp_s_84; static PyObject *__pyx_kp_s_85; -static PyObject *__pyx_n_s_87; +static PyObject *__pyx_kp_s_86; +static PyObject *__pyx_kp_s_87; static PyObject *__pyx_kp_s_88; static PyObject *__pyx_kp_s_89; -static PyObject *__pyx_kp_b_9; -static PyObject *__pyx_kp_s_9; -static PyObject *__pyx_n_s_90; +static PyObject *__pyx_n_s_9; +static PyObject *__pyx_kp_s_90; static PyObject *__pyx_kp_s_91; static PyObject *__pyx_kp_s_92; -static PyObject *__pyx_n_s_93; -static PyObject *__pyx_n_s_97; -static PyObject *__pyx_n_s_98; -static PyObject *__pyx_kp_b__0; +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; @@ -1415,7 +1402,6 @@ 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_b__PASS; static PyObject *__pyx_n_s__PASS; static PyObject *__pyx_n_s__POS; static PyObject *__pyx_n_s__POS_NOT_NUMERICAL; @@ -1468,7 +1454,6 @@ static PyObject *__pyx_n_s__alleleRegEx; static PyObject *__pyx_n_s__alt; static PyObject *__pyx_n_s__alt1; static PyObject *__pyx_n_s__alt2; -static PyObject *__pyx_n_s__append; static PyObject *__pyx_n_s__bisect; static PyObject *__pyx_n_s__buffer; static PyObject *__pyx_n_s__chrom; @@ -1480,7 +1465,6 @@ static PyObject *__pyx_n_s__contig; static PyObject *__pyx_n_s__convertGT; static PyObject *__pyx_n_s__convertGTback; static PyObject *__pyx_n_s__copy; -static PyObject *__pyx_n_s__cvcf; static PyObject *__pyx_n_s__data; static PyObject *__pyx_n_s__datagenerator; static PyObject *__pyx_n_s__deepcopy; @@ -1547,7 +1531,6 @@ static PyObject *__pyx_n_s__parse_format; 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; @@ -1633,70 +1616,14 @@ static PyObject *__pyx_int_33; static PyObject *__pyx_int_40; static PyObject *__pyx_int_100; static PyObject *__pyx_int_3000000000; -static PyObject *__pyx_k_22; -static PyObject *__pyx_k_26; -static PyObject *__pyx_k_60; -static PyObject *__pyx_k_64; -static PyObject *__pyx_k_65; -static PyObject *__pyx_k_99; -static PyObject *__pyx_k_tuple_3; -static PyObject *__pyx_k_tuple_5; -static PyObject *__pyx_k_tuple_7; -static PyObject *__pyx_k_tuple_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 +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 * * # Utility function. Uses 0-based coordinates * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<< @@ -1705,7 +1632,6 @@ static PyObject *__pyx_k_tuple_131; */ 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; @@ -1783,7 +1709,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p __pyx_L4_argument_unpacking_done:; __pyx_v_sequence = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":60 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":60 * def get_sequence(chrom, start, end, fa): * # obtain sequence from .fa file, without truncation * if end<=start: return "" # <<<<<<<<<<<<<< @@ -1803,7 +1729,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p } __pyx_L6:; - /* "cvcf.pyx":61 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":61 * # obtain sequence from .fa file, without truncation * if end<=start: return "" * if not fa: return "N"*(end-start) # <<<<<<<<<<<<<< @@ -1826,7 +1752,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p } __pyx_L7:; - /* "cvcf.pyx":62 + /* "/ifs/devel/pysam/pysam/pysam/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() # <<<<<<<<<<<<<< @@ -1847,7 +1773,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p __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(((PyObject *)__pyx_t_5)); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; @@ -1881,7 +1807,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p } __pyx_L8:; - /* "cvcf.pyx":63 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":63 * if not fa: return "N"*(end-start) * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() * sequence = fa.fetch(chrom, start, end).upper() # <<<<<<<<<<<<<< @@ -1891,7 +1817,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__p __pyx_t_5 = PyObject_GetAttr(__pyx_v_fa, __pyx_n_s__fetch); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_GOTREF(__pyx_t_6); 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return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_v_values = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); + __pyx_v_values = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_v_nmb = Py_None; __Pyx_INCREF(Py_None); __pyx_v_format = Py_None; __Pyx_INCREF(Py_None); __pyx_v_k = Py_None; __Pyx_INCREF(Py_None); __pyx_v_v = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":399 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":399 * * def format_format( self, fmt, filter=False ): * values = [('ID',fmt.id)] # <<<<<<<<<<<<<< @@ -6613,7 +6690,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(((PyObject *)__pyx_n_s__ID)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__ID)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID)); @@ -6622,14 +6699,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __pyx_t_1 = 0; __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); + PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_v_values)); __pyx_v_values = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":400 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":400 * def format_format( self, fmt, filter=False ): * values = [('ID',fmt.id)] * if fmt.number != None and not filter: # <<<<<<<<<<<<<< @@ -6652,7 +6729,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje } if (__pyx_t_4) { - /* "cvcf.pyx":401 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":401 * values = [('ID',fmt.id)] * if fmt.number != None and not filter: * if fmt.numbertype == self.NT_UNKNOWN: nmb = "." # <<<<<<<<<<<<<< @@ -6670,13 +6747,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); 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__pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __Pyx_GOTREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)&PyString_Type)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_v_nmb); __pyx_v_nmb = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L7; } - /* "cvcf.pyx":403 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":403 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "." * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" # <<<<<<<<<<<<<< @@ -6728,13 +6805,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); 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if (__pyx_t_4) { - __Pyx_INCREF(((PyObject *)__pyx_kp_s_57)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_29)); __Pyx_DECREF(__pyx_v_nmb); - __pyx_v_nmb = ((PyObject *)__pyx_kp_s_57); + __pyx_v_nmb = ((PyObject *)__pyx_kp_s_29); goto __pyx_L7; } - /* "cvcf.pyx":405 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":405 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" # <<<<<<<<<<<<<< @@ -6776,13 +6853,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (__pyx_t_4) { - __Pyx_INCREF(((PyObject *)__pyx_kp_s_58)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_30)); __Pyx_DECREF(__pyx_v_nmb); - __pyx_v_nmb = ((PyObject *)__pyx_kp_s_58); + __pyx_v_nmb = ((PyObject *)__pyx_kp_s_30); goto __pyx_L7; } - /* "cvcf.pyx":406 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":406 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" # <<<<<<<<<<<<<< @@ -6800,14 +6877,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_4) { - __Pyx_INCREF(((PyObject *)__pyx_kp_s_59)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_31)); __Pyx_DECREF(__pyx_v_nmb); - __pyx_v_nmb = ((PyObject *)__pyx_kp_s_59); + __pyx_v_nmb = ((PyObject *)__pyx_kp_s_31); goto __pyx_L7; } /*else*/ { - /* "cvcf.pyx":408 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":408 * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" * else: * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) # <<<<<<<<<<<<<< @@ -6816,24 +6893,24 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje */ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_1, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L7:; - /* "cvcf.pyx":409 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":409 * else: * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) * values.append( ('Number',nmb) ) # <<<<<<<<<<<<<< @@ -6844,17 +6921,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); 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__pyx_t_2 = 0; if (__pyx_t_4) { - /* "cvcf.pyx":413 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":413 * values.append( ('Description', '"' + fmt.description + '"') ) * if self._version == 33: * format = ",".join([v for k,v in values]) # <<<<<<<<<<<<<< @@ -6936,10 +7013,11 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - if (unlikely(__pyx_v_values == Py_None)) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (likely(((PyObject *)__pyx_v_values) != Py_None)) { + __pyx_t_8 = 0; __pyx_t_6 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_6); + } else { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_8 = 0; __pyx_t_6 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_6); for (;;) { if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_6)) break; __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; @@ -6975,15 +7053,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(((PyObject *)__pyx_t_1)); PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_2, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_v_format); __pyx_v_format = __pyx_t_1; __pyx_t_1 = 0; @@ -6991,7 +7069,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje } /*else*/ { - /* "cvcf.pyx":415 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":415 * format = ",".join([v for k,v in values]) * else: * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" # <<<<<<<<<<<<<< @@ -7002,10 +7080,11 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje __Pyx_GOTREF(__pyx_t_1); __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; 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__Pyx_DECREF(__pyx_v_format); @@ -7074,7 +7153,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje } __pyx_L8:; - /* "cvcf.pyx":416 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":416 * else: * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" * return format # <<<<<<<<<<<<<< @@ -7109,7 +7188,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje return __pyx_r; } -/* "cvcf.pyx":418 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":418 * return format * * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<< @@ -7117,9 +7196,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_3format_format(PyObject *__pyx_self, PyObje * if fmt.numbertype == self.NT_UNKNOWN: return -1 */ -static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_4get_expected = {__Pyx_NAMESTR("get_expected"), (PyCFunction)__pyx_pf_4cvcf_3VCF_4get_expected, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_get_expected = {__Pyx_NAMESTR("get_expected"), (PyCFunction)__pyx_pf_4cvcf_3VCF_get_expected, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_format = 0; PyObject *__pyx_v_formatdict = 0; @@ -7195,7 +7274,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec __pyx_L4_argument_unpacking_done:; __pyx_v_fmt = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":419 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":419 * * def get_expected(self, format, formatdict, alt): * fmt = formatdict[format] # <<<<<<<<<<<<<< @@ -7208,7 +7287,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec __pyx_v_fmt = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":420 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":420 * def get_expected(self, format, formatdict, alt): * fmt = formatdict[format] * if fmt.numbertype == self.NT_UNKNOWN: return -1 # <<<<<<<<<<<<<< @@ -7234,7 +7313,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec } __pyx_L6:; - /* "cvcf.pyx":421 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":421 * fmt = formatdict[format] * if fmt.numbertype == self.NT_UNKNOWN: return -1 * if fmt.numbertype == self.NT_NUMBER: return fmt.number # <<<<<<<<<<<<<< @@ -7262,7 +7341,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec } __pyx_L7:; - /* "cvcf.pyx":422 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":422 * if fmt.numbertype == self.NT_UNKNOWN: return -1 * if fmt.numbertype == self.NT_NUMBER: return fmt.number * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 # <<<<<<<<<<<<<< @@ -7291,7 +7370,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec } __pyx_L8:; - /* "cvcf.pyx":423 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":423 * if fmt.numbertype == self.NT_NUMBER: return fmt.number * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) # <<<<<<<<<<<<<< @@ -7320,7 +7399,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec } __pyx_L9:; - /* "cvcf.pyx":424 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":424 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 # <<<<<<<<<<<<<< @@ -7350,7 +7429,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec } __pyx_L10:; - /* "cvcf.pyx":425 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":425 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) # <<<<<<<<<<<<<< @@ -7380,7 +7459,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec } __pyx_L11:; - /* "cvcf.pyx":426 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":426 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) * return 0 # <<<<<<<<<<<<<< @@ -7407,7 +7486,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec return __pyx_r; } -/* "cvcf.pyx":429 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":429 * * * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<< @@ -7415,9 +7494,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4get_expected(PyObject *__pyx_self, PyObjec * self.error(line,self.ERROR_UNKNOWN_KEY,key) */ -static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_5_add_definition = {__Pyx_NAMESTR("_add_definition"), (PyCFunction)__pyx_pf_4cvcf_3VCF_5_add_definition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF__add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF__add_definition = {__Pyx_NAMESTR("_add_definition"), (PyCFunction)__pyx_pf_4cvcf_3VCF__add_definition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF__add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_formatdict = 0; PyObject *__pyx_v_key = 0; @@ -7500,7 +7579,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __pyx_L4_argument_unpacking_done:; __Pyx_INCREF(__pyx_v_data); - /* "cvcf.pyx":430 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":430 * * def _add_definition(self, formatdict, key, data, line ): * if key in formatdict: return # <<<<<<<<<<<<<< @@ -7516,7 +7595,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb } __pyx_L6:; - /* "cvcf.pyx":431 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":431 * def _add_definition(self, formatdict, key, data, line ): * if key in formatdict: return * self.error(line,self.ERROR_UNKNOWN_KEY,key) # <<<<<<<<<<<<<< @@ -7528,7 +7607,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_UNKNOWN_KEY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_4)); + __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); @@ -7538,13 +7617,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":432 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":432 * if key in formatdict: return * self.error(line,self.ERROR_UNKNOWN_KEY,key) * if data == None: # <<<<<<<<<<<<<< @@ -7557,7 +7636,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_1) { - /* "cvcf.pyx":433 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":433 * self.error(line,self.ERROR_UNKNOWN_KEY,key) * if data == None: * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") # <<<<<<<<<<<<<< @@ -7569,7 +7648,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -7581,21 +7660,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_INCREF(((PyObject *)__pyx_n_s__Flag)); PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__Flag)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Flag)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_63)); - PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); - PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_35)); + PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_35)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_6)); + PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_6)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6)); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":434 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":434 * if data == None: * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") * return # <<<<<<<<<<<<<< @@ -7609,7 +7688,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb } __pyx_L7:; - /* "cvcf.pyx":435 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":435 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") * return * if data == []: data = [""] # unsure what type -- say string # <<<<<<<<<<<<<< @@ -7636,7 +7715,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb } __pyx_L8:; - /* "cvcf.pyx":436 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":436 * return * if data == []: data = [""] # unsure what type -- say string * if type(data[0]) == type(0.0): # <<<<<<<<<<<<<< @@ -7655,7 +7734,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_1) { - /* "cvcf.pyx":437 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":437 * if data == []: data = [""] # unsure what type -- say string * if type(data[0]) == type(0.0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) # <<<<<<<<<<<<<< @@ -7667,7 +7746,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -7679,21 +7758,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_INCREF(((PyObject *)__pyx_n_s__Float)); PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__Float)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Float)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_63)); - PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_35)); + PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_35)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35)); __Pyx_INCREF(Py_None); PyTuple_SET_ITEM(__pyx_t_2, 5, Py_None); __Pyx_GIVEREF(Py_None); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":438 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":438 * if type(data[0]) == type(0.0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) * return # <<<<<<<<<<<<<< @@ -7707,7 +7786,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb } __pyx_L9:; - /* "cvcf.pyx":439 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":439 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) * return * if type(data[0]) == type(0): # <<<<<<<<<<<<<< @@ -7723,7 +7802,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_1) { - /* "cvcf.pyx":440 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":440 * return * if type(data[0]) == type(0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) # <<<<<<<<<<<<<< @@ -7735,7 +7814,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -7747,21 +7826,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_INCREF(((PyObject *)__pyx_n_s__Integer)); PyTuple_SET_ITEM(__pyx_t_3, 3, ((PyObject *)__pyx_n_s__Integer)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Integer)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_63)); - PyTuple_SET_ITEM(__pyx_t_3, 4, ((PyObject *)__pyx_kp_s_63)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_35)); + PyTuple_SET_ITEM(__pyx_t_3, 4, ((PyObject *)__pyx_kp_s_35)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35)); 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- /* "cvcf.pyx":442 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":442 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) * return * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # <<<<<<<<<<<<<< @@ -7787,7 +7866,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -7799,17 +7878,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb __Pyx_INCREF(((PyObject *)__pyx_n_s__String)); PyTuple_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_n_s__String)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__String)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_63)); - PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_63)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_63)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); - PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_35)); + PyTuple_SET_ITEM(__pyx_t_2, 4, ((PyObject *)__pyx_kp_s_35)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_35)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_6)); + PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_6)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6)); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Call(__pyx_t_4, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -7828,7 +7907,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb return __pyx_r; } -/* "cvcf.pyx":446 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":446 * * # todo: trim trailing missing values * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<< @@ -7836,9 +7915,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_5_add_definition(PyObject *__pyx_self, PyOb * if type(data) == type([]): # for FORMAT field, make data with dummy values */ -static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_6format_formatdata = {__Pyx_NAMESTR("format_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_6format_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_format_formatdata = {__Pyx_NAMESTR("format_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_format_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_data = 0; PyObject *__pyx_v_format = 0; @@ -7870,9 +7949,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); PyObject* values[6] = {0,0,0,0,0,0}; - values[3] = __pyx_k_64; - values[4] = __pyx_k_65; - values[5] = ((PyObject *)__pyx_kp_s_4); + values[3] = __pyx_k_36; + values[4] = __pyx_k_37; + values[5] = ((PyObject *)__pyx_kp_s_3); switch (PyTuple_GET_SIZE(__pyx_args)) { case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); @@ -7926,9 +8005,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_v_value = values[4]; __pyx_v_separator = values[5]; } else { - __pyx_v_key = __pyx_k_64; - __pyx_v_value = __pyx_k_65; - __pyx_v_separator = ((PyObject *)__pyx_kp_s_4); + __pyx_v_key = __pyx_k_36; + __pyx_v_value = __pyx_k_37; + __pyx_v_separator = ((PyObject *)__pyx_kp_s_3); switch (PyTuple_GET_SIZE(__pyx_args)) { case 6: __pyx_v_separator = PyTuple_GET_ITEM(__pyx_args, 5); @@ -7953,15 +8032,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py return NULL; __pyx_L4_argument_unpacking_done:; __Pyx_INCREF(__pyx_v_data); - __pyx_v_output = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); - __pyx_v_sdata = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); - __pyx_v_d = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); + __pyx_v_output = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); + __pyx_v_sdata = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); + __pyx_v_d = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_v_k = Py_None; __Pyx_INCREF(Py_None); __pyx_v_idx = Py_None; __Pyx_INCREF(Py_None); __pyx_v_v = Py_None; __Pyx_INCREF(Py_None); __pyx_v_last = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":447 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":447 * # todo: trim trailing missing values * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): * output, sdata = [], [] # <<<<<<<<<<<<<< @@ -7979,7 +8058,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_v_sdata = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":448 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":448 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): * output, sdata = [], [] * if type(data) == type([]): # for FORMAT field, make data with dummy values # <<<<<<<<<<<<<< @@ -7995,7 +8074,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":449 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":449 * output, sdata = [], [] * if type(data) == type([]): # for FORMAT field, make data with dummy values * d = {} # <<<<<<<<<<<<<< @@ -8008,7 +8087,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_v_d = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":450 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":450 * if type(data) == type([]): # for FORMAT field, make data with dummy values * d = {} * for k in data: d[k] = [] # <<<<<<<<<<<<<< @@ -8046,7 +8125,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":451 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":451 * d = {} * for k in data: d[k] = [] * data = d # <<<<<<<<<<<<<< @@ -8060,7 +8139,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py } __pyx_L6:; - /* "cvcf.pyx":453 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":453 * data = d * # convert missing values; 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__Pyx_GIVEREF(__pyx_v_format); @@ -8113,17 +8192,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __Pyx_GIVEREF(__pyx_v_k); PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_66)); - PyTuple_SET_ITEM(__pyx_t_6, 3, ((PyObject *)__pyx_kp_s_66)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_38)); + PyTuple_SET_ITEM(__pyx_t_6, 3, ((PyObject *)__pyx_kp_s_38)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_38)); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(__pyx_t_2, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":455 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":455 * for k in data: * self._add_definition( format, k, data[k], "(output)" ) * for idx,v in enumerate(data[k]): # <<<<<<<<<<<<<< @@ -8168,7 +8247,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_t_5 = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":456 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":456 * self._add_definition( format, k, data[k], "(output)" ) * for idx,v in enumerate(data[k]): * if v == format[k].missingvalue: data[k][idx] = "." # <<<<<<<<<<<<<< @@ -8188,7 +8267,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py if (__pyx_t_3) { __pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (PyObject_SetItem(__pyx_t_6, __pyx_v_idx, ((PyObject *)__pyx_kp_s_9)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetItem(__pyx_t_6, __pyx_v_idx, ((PyObject *)__pyx_kp_s_6)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; goto __pyx_L13; } @@ -8199,7 +8278,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":458 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":458 * if v == format[k].missingvalue: data[k][idx] = "." * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string * for k in data: # <<<<<<<<<<<<<< @@ -8231,7 +8310,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_v_k = __pyx_t_5; __pyx_t_5 = 0; - /* "cvcf.pyx":459 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":459 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string * for k in data: * if k != 'GT': sdata.append( (k,data[k]) ) # <<<<<<<<<<<<<< @@ -8249,22 +8328,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_t_5 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_k); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_k); __Pyx_GIVEREF(__pyx_v_k); PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_9 = PyList_Append(__pyx_v_sdata, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __pyx_t_9 = PyList_Append(((PyObject *)__pyx_v_sdata), __pyx_t_2); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L16; } __pyx_L16:; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":460 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":460 * for k in data: * if k != 'GT': sdata.append( (k,data[k]) ) * sdata.sort() # <<<<<<<<<<<<<< @@ -8276,7 +8355,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py } __pyx_t_9 = PyList_Sort(((PyObject *)__pyx_v_sdata)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":461 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":461 * if k != 'GT': sdata.append( (k,data[k]) ) * sdata.sort() * if 'GT' in data: # <<<<<<<<<<<<<< @@ -8286,7 +8365,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_t_3 = ((PySequence_Contains(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_3) { - /* "cvcf.pyx":462 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":462 * sdata.sort() * if 'GT' in data: * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata # <<<<<<<<<<<<<< @@ -8298,18 +8377,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_formatdata(PyObject *__pyx_self, Py __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)); 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} else { __pyx_t_9 = PyIter_Next(__pyx_t_10); if (!__pyx_t_9) { @@ -10321,47 +10457,47 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10parse_heading(PyObject *__pyx_self, PyObj __Pyx_DECREF(__pyx_v_y); __pyx_v_y = __pyx_t_9; __pyx_t_9 = 0; - __Pyx_INCREF(__pyx_t_1); + __Pyx_INCREF(__pyx_t_3); __Pyx_DECREF(__pyx_v_x); - __pyx_v_x = __pyx_t_1; - __pyx_t_9 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_x = __pyx_t_3; + __pyx_t_9 = PyNumber_Add(__pyx_t_3, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_1); - __pyx_t_1 = __pyx_t_9; + __Pyx_DECREF(__pyx_t_3); + __pyx_t_3 = __pyx_t_9; __pyx_t_9 = 0; __pyx_t_9 = PyNumber_Add(__pyx_v_x, __pyx_int_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; 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__pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __Pyx_INCREF(((PyObject *)__pyx_t_2)); - PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyDict_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_INCREF(((PyObject *)__pyx_t_1)); + PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)&PyDict_Type)), __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_9); __Pyx_XDECREF(__pyx_t_10); __Pyx_AddTraceback("cvcf.VCF.parse_heading"); @@ -10378,7 +10514,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10parse_heading(PyObject *__pyx_self, PyObj return __pyx_r; } -/* "cvcf.pyx":553 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":553 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) * * def write_heading( self, stream ): # <<<<<<<<<<<<<< @@ -10386,9 +10522,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10parse_heading(PyObject *__pyx_self, PyObj * */ -static PyObject *__pyx_pf_4cvcf_3VCF_11write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_11write_heading = {__Pyx_NAMESTR("write_heading"), (PyCFunction)__pyx_pf_4cvcf_3VCF_11write_heading, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_11write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_write_heading = {__Pyx_NAMESTR("write_heading"), (PyCFunction)__pyx_pf_4cvcf_3VCF_write_heading, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; PyObject *__pyx_r = NULL; @@ -10441,7 +10577,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_11write_heading(PyObject *__pyx_self, PyObj return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":554 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":554 * * def write_heading( self, stream ): * stream.write("#" + "\t".join(self._required + self._samples) + "\n") # <<<<<<<<<<<<<< @@ -10450,7 +10586,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_11write_heading(PyObject *__pyx_self, PyObj */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; 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goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_4)); + __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; - __pyx_t_4 = PyNumber_Add(((PyObject *)__pyx_kp_s_82), __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = PyNumber_Add(((PyObject *)__pyx_kp_s_50), __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyNumber_Add(__pyx_t_4, ((PyObject *)__pyx_kp_s_91)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_Add(__pyx_t_4, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_4)); + __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(__pyx_t_1, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -10502,7 +10638,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_11write_heading(PyObject *__pyx_self, PyObj return __pyx_r; } -/* "cvcf.pyx":556 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":556 * stream.write("#" + "\t".join(self._required + self._samples) + "\n") * * def convertGT(self, GTstring): # <<<<<<<<<<<<<< @@ -10510,9 +10646,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_11write_heading(PyObject *__pyx_self, PyObj * try: */ -static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_12convertGT = {__Pyx_NAMESTR("convertGT"), (PyCFunction)__pyx_pf_4cvcf_3VCF_12convertGT, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_convertGT = {__Pyx_NAMESTR("convertGT"), (PyCFunction)__pyx_pf_4cvcf_3VCF_convertGT, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_GTstring = 0; PyObject *__pyx_v_gts; @@ -10575,14 +10711,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject __pyx_L4_argument_unpacking_done:; __pyx_v_gts = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":557 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":557 * * def convertGT(self, GTstring): * if GTstring == ".": return ["."] # <<<<<<<<<<<<<< * try: * gts = gtsRegEx.split(GTstring) */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_6), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -10590,9 +10726,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); - PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_9)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_6)); + PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_6)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6)); __pyx_r = ((PyObject *)__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; @@ -10600,7 +10736,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject } __pyx_L6:; - /* "cvcf.pyx":558 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":558 * def convertGT(self, GTstring): * if GTstring == ".": return ["."] * try: # <<<<<<<<<<<<<< @@ -10615,7 +10751,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject __Pyx_XGOTREF(__pyx_save_exc_tb); /*try:*/ { - /* "cvcf.pyx":559 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":559 * if GTstring == ".": return ["."] * try: * gts = gtsRegEx.split(GTstring) # <<<<<<<<<<<<<< @@ -10628,19 +10764,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(1); 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if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __Pyx_GOTREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)&PyInt_Type)), __pyx_t_1, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_4); @@ -10673,7 +10809,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject } __pyx_L15:; - /* "cvcf.pyx":561 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":561 * gts = gtsRegEx.split(GTstring) * if len(gts) == 1: return [int(gts[0])] * if len(gts) != 2: raise ValueError() # <<<<<<<<<<<<<< @@ -10692,7 +10828,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject } __pyx_L16:; - /* "cvcf.pyx":562 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":562 * if len(gts) == 1: return [int(gts[0])] * if len(gts) != 2: raise ValueError() * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] # <<<<<<<<<<<<<< @@ -10701,7 +10837,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject */ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_4 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_4 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_kp_s_6), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} @@ -10709,7 +10845,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject if (__pyx_t_2) { __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_4, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_t_4, ((PyObject *)__pyx_kp_s_6), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L7_error;} @@ -10730,7 +10866,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12convertGT(PyObject *__pyx_self, PyObject __Pyx_GOTREF(__pyx_t_4); __pyx_t_8 = PyObject_Length(__pyx_t_4); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; 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/*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_convertGTback = {__Pyx_NAMESTR("convertGTback"), (PyCFunction)__pyx_pf_4cvcf_3VCF_convertGTback, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_GTdata = 0; PyObject *__pyx_r = NULL; @@ -10996,7 +11132,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObj return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":570 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":570 * * def convertGTback(self, GTdata): * return ''.join(map(str,GTdata)) # <<<<<<<<<<<<<< @@ -11007,25 +11143,25 @@ static PyObject *__pyx_pf_4cvcf_3VCF_13convertGTback(PyObject *__pyx_self, PyObj __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); 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/*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_parse_formatdata = {__Pyx_NAMESTR("parse_formatdata"), (PyCFunction)__pyx_pf_4cvcf_3VCF_parse_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_key = 0; PyObject *__pyx_v_value = 0; @@ -11154,7 +11290,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py __pyx_v_idx = Py_None; __Pyx_INCREF(Py_None); __pyx_v_v = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":574 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":574 * def parse_formatdata( self, key, value, formatdict, line ): * # To do: check that the right number of values is present * f = formatdict.get(key,None) # <<<<<<<<<<<<<< @@ -11164,22 +11300,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14parse_formatdata(PyObject *__pyx_self, Py __pyx_t_1 = PyObject_GetAttr(__pyx_v_formatdict, __pyx_n_s__get); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_v_d); __pyx_v_d = __pyx_t_2; __pyx_t_2 = 0; @@ -17660,7 +17881,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__ return __pyx_r; } -/* "cvcf.pyx":880 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":880 * ###################################################################################################### * * def getsamples(self): # <<<<<<<<<<<<<< @@ -17668,16 +17889,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_19_parse(PyObject *__pyx_self, PyObject *__ * return self._samples */ -static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_20getsamples[] = " List of samples in VCF file "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_20getsamples = {__Pyx_NAMESTR("getsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_20getsamples, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_20getsamples)}; -static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_4cvcf_3VCF_getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_getsamples[] = " List of samples in VCF file "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_getsamples = {__Pyx_NAMESTR("getsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getsamples, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getsamples)}; +static PyObject *__pyx_pf_4cvcf_3VCF_getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("getsamples"); __pyx_self = __pyx_self; - /* "cvcf.pyx":882 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":882 * def getsamples(self): * """ List of samples in VCF file """ * return self._samples # <<<<<<<<<<<<<< @@ -17703,7 +17924,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":884 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":884 * return self._samples * * def setsamples(self,samples): # <<<<<<<<<<<<<< @@ -17711,10 +17932,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20getsamples(PyObject *__pyx_self, PyObject * self._samples = samples */ -static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_21setsamples[] = " List of samples in VCF file "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_21setsamples = {__Pyx_NAMESTR("setsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_21setsamples, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_21setsamples)}; -static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_setsamples[] = " List of samples in VCF file "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setsamples = {__Pyx_NAMESTR("setsamples"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setsamples, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setsamples)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_samples = 0; PyObject *__pyx_r = NULL; @@ -17762,7 +17983,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":886 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":886 * def setsamples(self,samples): * """ List of samples in VCF file """ * self._samples = samples # <<<<<<<<<<<<<< @@ -17782,7 +18003,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":888 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":888 * self._samples = samples * * def getheader(self): # <<<<<<<<<<<<<< @@ -17790,16 +18011,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_21setsamples(PyObject *__pyx_self, PyObject * return self._header */ -static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_22getheader[] = " List of header key-value pairs (strings) "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_22getheader = {__Pyx_NAMESTR("getheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_22getheader, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_22getheader)}; -static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_4cvcf_3VCF_getheader(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_getheader[] = " List of header key-value pairs (strings) "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_getheader = {__Pyx_NAMESTR("getheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getheader, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getheader)}; +static PyObject *__pyx_pf_4cvcf_3VCF_getheader(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("getheader"); __pyx_self = __pyx_self; - /* "cvcf.pyx":890 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":890 * def getheader(self): * """ List of header key-value pairs (strings) """ * return self._header # <<<<<<<<<<<<<< @@ -17825,7 +18046,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":892 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":892 * return self._header * * def setheader(self,header): # <<<<<<<<<<<<<< @@ -17833,10 +18054,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22getheader(PyObject *__pyx_self, PyObject * self._header = header */ -static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_23setheader[] = " List of header key-value pairs (strings) "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_23setheader = {__Pyx_NAMESTR("setheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_23setheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_23setheader)}; -static PyObject *__pyx_pf_4cvcf_3VCF_23setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_setheader[] = " List of header key-value pairs (strings) "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setheader = {__Pyx_NAMESTR("setheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setheader)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_header = 0; 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-static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_4cvcf_3VCF_getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_getinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_getinfo = {__Pyx_NAMESTR("getinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getinfo, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getinfo)}; +static PyObject *__pyx_pf_4cvcf_3VCF_getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("getinfo"); __pyx_self = __pyx_self; - /* "cvcf.pyx":898 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":898 * def getinfo(self): * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * return self._info # <<<<<<<<<<<<<< @@ -17947,7 +18168,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *_ return __pyx_r; } -/* "cvcf.pyx":900 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":900 * return self._info * * def setinfo(self,info): # <<<<<<<<<<<<<< @@ -17955,10 +18176,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24getinfo(PyObject *__pyx_self, PyObject *_ * self._info = info */ -static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_25setinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_25setinfo = {__Pyx_NAMESTR("setinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_25setinfo, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_25setinfo)}; -static PyObject *__pyx_pf_4cvcf_3VCF_25setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_setinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setinfo = {__Pyx_NAMESTR("setinfo"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setinfo, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setinfo)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_info = 0; 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-static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_4cvcf_3VCF_getformat(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_getformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_getformat = {__Pyx_NAMESTR("getformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getformat, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getformat)}; +static PyObject *__pyx_pf_4cvcf_3VCF_getformat(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("getformat"); __pyx_self = __pyx_self; - /* "cvcf.pyx":906 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":906 * def getformat(self): * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * return self._format # <<<<<<<<<<<<<< @@ -18069,7 +18290,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":908 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":908 * return self._format * * def setformat(self,format): # <<<<<<<<<<<<<< @@ -18077,10 +18298,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26getformat(PyObject *__pyx_self, PyObject * self._format = format */ -static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_27setformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_27setformat = {__Pyx_NAMESTR("setformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_27setformat, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_27setformat)}; -static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_setformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setformat = {__Pyx_NAMESTR("setformat"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setformat, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setformat)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_format = 0; PyObject *__pyx_r = NULL; @@ -18128,7 +18349,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":910 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":910 * def setformat(self,format): * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * self._format = format # <<<<<<<<<<<<<< @@ -18148,7 +18369,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":912 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":912 * self._format = format * * def getfilter(self): # <<<<<<<<<<<<<< @@ -18156,16 +18377,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_27setformat(PyObject *__pyx_self, PyObject * return self._filter */ -static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_28getfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_28getfilter = {__Pyx_NAMESTR("getfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_28getfilter, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_28getfilter)}; -static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_4cvcf_3VCF_getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_getfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_getfilter = {__Pyx_NAMESTR("getfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_getfilter, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_getfilter)}; +static PyObject *__pyx_pf_4cvcf_3VCF_getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_RefNannySetupContext("getfilter"); __pyx_self = __pyx_self; - /* "cvcf.pyx":914 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":914 * def getfilter(self): * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * return self._filter # <<<<<<<<<<<<<< @@ -18191,7 +18412,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":916 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":916 * return self._filter * * def setfilter(self,filter): # <<<<<<<<<<<<<< @@ -18199,10 +18420,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28getfilter(PyObject *__pyx_self, PyObject * self._filter = filter */ -static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_29setfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_29setfilter = {__Pyx_NAMESTR("setfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_29setfilter, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_29setfilter)}; -static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_setfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setfilter = {__Pyx_NAMESTR("setfilter"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setfilter, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setfilter)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_filter = 0; PyObject *__pyx_r = NULL; @@ -18250,7 +18471,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":918 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":918 * def setfilter(self,filter): * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * self._filter = filter # <<<<<<<<<<<<<< @@ -18270,7 +18491,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":920 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":920 * self._filter = filter * * def setversion(self, version): # <<<<<<<<<<<<<< @@ -18278,9 +18499,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_29setfilter(PyObject *__pyx_self, PyObject * self._version = version */ -static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_30setversion = {__Pyx_NAMESTR("setversion"), (PyCFunction)__pyx_pf_4cvcf_3VCF_30setversion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setversion = {__Pyx_NAMESTR("setversion"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setversion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_version = 0; PyObject *__pyx_r = NULL; @@ -18288,6 +18509,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0}; __Pyx_RefNannySetupContext("setversion"); __pyx_self = __pyx_self; @@ -18332,7 +18554,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":921 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":921 * * def setversion(self, version): * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<< @@ -18353,16 +18575,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject __pyx_t_4 = __pyx_t_2; } if (__pyx_t_4) { - __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_120), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_Raise(__pyx_t_1, 0, 0); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_70)); + PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_70)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_70)); + __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_Raise(__pyx_t_5, 0, 0); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; - /* "cvcf.pyx":922 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":922 * def setversion(self, version): * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") * self._version = version # <<<<<<<<<<<<<< @@ -18375,6 +18603,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_5); __Pyx_AddTraceback("cvcf.VCF.setversion"); __pyx_r = NULL; __pyx_L0:; @@ -18383,7 +18612,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":924 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":924 * self._version = version * * def setregions(self, regions): # <<<<<<<<<<<<<< @@ -18391,9 +18620,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30setversion(PyObject *__pyx_self, PyObject * */ -static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_31setregions = {__Pyx_NAMESTR("setregions"), (PyCFunction)__pyx_pf_4cvcf_3VCF_31setregions, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setregions = {__Pyx_NAMESTR("setregions"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setregions, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_regions = 0; PyObject *__pyx_r = NULL; @@ -18441,7 +18670,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":925 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":925 * * def setregions(self, regions): * self._regions = regions # <<<<<<<<<<<<<< @@ -18461,7 +18690,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "cvcf.pyx":927 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":927 * self._regions = regions * * def setreference(self, ref): # <<<<<<<<<<<<<< @@ -18469,10 +18698,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_31setregions(PyObject *__pyx_self, PyObject * self._reference = ref */ -static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_32setreference[] = " Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_32setreference = {__Pyx_NAMESTR("setreference"), (PyCFunction)__pyx_pf_4cvcf_3VCF_32setreference, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_32setreference)}; -static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_setreference[] = " Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_setreference = {__Pyx_NAMESTR("setreference"), (PyCFunction)__pyx_pf_4cvcf_3VCF_setreference, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_setreference)}; +static PyObject *__pyx_pf_4cvcf_3VCF_setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_ref = 0; PyObject *__pyx_r = NULL; @@ -18520,7 +18749,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObje return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":929 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":929 * def setreference(self, ref): * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ * self._reference = ref # <<<<<<<<<<<<<< @@ -18540,7 +18769,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObje return __pyx_r; } -/* "cvcf.pyx":931 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":931 * self._reference = ref * * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<< @@ -18548,9 +18777,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32setreference(PyObject *__pyx_self, PyObje * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ -static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_33ignoreerror = {__Pyx_NAMESTR("ignoreerror"), (PyCFunction)__pyx_pf_4cvcf_3VCF_33ignoreerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_4cvcf_3VCF_ignoreerror = {__Pyx_NAMESTR("ignoreerror"), (PyCFunction)__pyx_pf_4cvcf_3VCF_ignoreerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pf_4cvcf_3VCF_ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_errorstring = 0; PyObject *__pyx_r = NULL; @@ -18604,7 +18833,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":932 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":932 * * def ignoreerror(self, errorstring): * try: self._ignored_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<< @@ -18629,14 +18858,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L6_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __Pyx_GOTREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L6_error;} + __pyx_t_3 = PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L6_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0; @@ -18648,7 +18877,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":933 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":933 * def ignoreerror(self, errorstring): * try: self._ignored_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<< @@ -18662,16 +18891,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec __Pyx_GOTREF(__pyx_t_3); 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__pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} + __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_Raise(__pyx_t_5, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} @@ -18710,7 +18939,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec return __pyx_r; } -/* "cvcf.pyx":935 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":935 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def warnerror(self, errorstring): # <<<<<<<<<<<<<< @@ -18718,9 +18947,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_33ignoreerror(PyObject *__pyx_self, PyObjec * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ -static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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__pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5)); __Pyx_GIVEREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} + __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_Raise(__pyx_t_5, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L8_except_error;} @@ -18880,7 +19109,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34warnerror(PyObject *__pyx_self, PyObject return __pyx_r; 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Initializes class instance and return generator "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_parse = {__Pyx_NAMESTR("parse"), (PyCFunction)__pyx_pf_4cvcf_3VCF_parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_parse)}; +static PyObject *__pyx_pf_4cvcf_3VCF_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; PyObject *__pyx_v_last_line; @@ -18944,7 +19173,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p __pyx_L4_argument_unpacking_done:; __pyx_v_last_line = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":941 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":941 * def parse(self, stream): * """ Parse a stream of VCF-formatted lines. 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__pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_3, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; @@ -19007,7 +19236,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p return __pyx_r; } -/* "cvcf.pyx":946 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":946 * return self._parse(last_line, stream) * * def write(self, stream, datagenerator): # <<<<<<<<<<<<<< @@ -19015,10 +19244,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_35parse(PyObject *__pyx_self, PyObject *__p * self.write_header(stream) */ -static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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PyObject *__pyx_v_datagenerator = 0; @@ -19083,7 +19312,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p __pyx_L4_argument_unpacking_done:; __pyx_v_data = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":948 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":948 * def write(self, stream, datagenerator): * """ Writes a VCF file to a stream, using a data generator (or list) """ * self.write_header(stream) # <<<<<<<<<<<<<< @@ -19093,17 +19322,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_stream); 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__pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":950 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":950 * self.write_header(stream) * self.write_heading(stream) * for data in datagenerator: self.write_data(stream,data) # <<<<<<<<<<<<<< @@ -19157,17 +19386,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36write(PyObject *__pyx_self, PyObject *__p __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_data); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_v_stream); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stream); __Pyx_GIVEREF(__pyx_v_stream); __Pyx_INCREF(__pyx_v_data); PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_data); __Pyx_GIVEREF(__pyx_v_data); 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/*proto*/ -static char __pyx_doc_4cvcf_3VCF_37writeheader[] = " Writes a VCF header "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_37writeheader = {__Pyx_NAMESTR("writeheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_37writeheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_37writeheader)}; -static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_writeheader[] = " Writes a VCF header "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_writeheader = {__Pyx_NAMESTR("writeheader"), (PyCFunction)__pyx_pf_4cvcf_3VCF_writeheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_writeheader)}; +static PyObject *__pyx_pf_4cvcf_3VCF_writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; PyObject *__pyx_r = NULL; @@ -19250,7 +19479,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":954 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":954 * def writeheader(self, stream): * """ Writes a VCF header """ * self.write_header(stream) # <<<<<<<<<<<<<< @@ -19260,17 +19489,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_stream); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream); __Pyx_GIVEREF(__pyx_v_stream); 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__Pyx_INCREF(Py_None); @@ -19304,7 +19533,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec return __pyx_r; } -/* "cvcf.pyx":957 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":957 * self.write_heading(stream) * * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<< @@ -19312,10 +19541,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_37writeheader(PyObject *__pyx_self, PyObjec * # a variant should always be assigned to a unique position, one base before */ -static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_38compare_calls[] = " Utility function: compares two calls for equality "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_38compare_calls = {__Pyx_NAMESTR("compare_calls"), (PyCFunction)__pyx_pf_4cvcf_3VCF_38compare_calls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_38compare_calls)}; -static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_compare_calls[] = " Utility function: compares two calls for equality "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_compare_calls = {__Pyx_NAMESTR("compare_calls"), (PyCFunction)__pyx_pf_4cvcf_3VCF_compare_calls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_compare_calls)}; +static PyObject *__pyx_pf_4cvcf_3VCF_compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_pos1 = 0; PyObject *__pyx_v_ref1 = 0; @@ -19425,7 +19654,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj __Pyx_INCREF(__pyx_v_ref2); __Pyx_INCREF(__pyx_v_alt2); - /* "cvcf.pyx":962 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":962 * # the leftmost position of the alignment gap. 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__pyx_t_6 = 0; - /* "cvcf.pyx":967 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":967 * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: * ref1 = ref1[:-1] * alt1 = alt1[:-1] # <<<<<<<<<<<<<< * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: * ref2 = ref2[:-1] */ - __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_alt1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_GetSlice(__pyx_v_alt1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_v_alt1); __pyx_v_alt1 = __pyx_t_6; __pyx_t_6 = 0; } - /* "cvcf.pyx":968 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":968 * ref1 = ref1[:-1] * alt1 = alt1[:-1] * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: # <<<<<<<<<<<<<< @@ -19542,34 +19771,34 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj } if (!__pyx_t_2) break; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PySequence_GetSlice(__pyx_v_alt2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_v_alt2); __pyx_v_alt2 = __pyx_t_1; __pyx_t_1 = 0; } - /* "cvcf.pyx":972 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":972 * alt2 = alt2[:-1] * # now, the alternative alleles must be identical * return alt1 == alt2 # <<<<<<<<<<<<<< @@ -19601,7 +19830,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj return __pyx_r; } -/* "cvcf.pyx":979 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":979 * ########################################################################################################### * * def connect( self, filename ): # <<<<<<<<<<<<<< @@ -19609,10 +19838,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38compare_calls(PyObject *__pyx_self, PyObj * self.tabixfile = pysam.Tabixfile( filename ) */ -static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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+ __Pyx_GOTREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -19726,7 +19955,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_ return __pyx_r; } -/* "cvcf.pyx":984 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":984 * self._parse_header(self.tabixfile.header) * * def fetch(self, # <<<<<<<<<<<<<< @@ -19734,10 +19963,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_39connect(PyObject *__pyx_self, PyObject *_ * start = None, */ -static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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Initializes class instance and return generator "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_40fetch = {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_4cvcf_3VCF_40fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_40fetch)}; -static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_fetch[] = " Parse a stream of VCF-formatted lines. Initializes class instance and return generator "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_fetch = {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_4cvcf_3VCF_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_fetch)}; +static PyObject *__pyx_pf_4cvcf_3VCF_fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; @@ -19756,7 +19985,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); PyObject* values[5] = {0,0,0,0,0}; - /* "cvcf.pyx":985 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":985 * * def fetch(self, * reference = None, # <<<<<<<<<<<<<< @@ -19765,7 +19994,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p */ values[1] = ((PyObject *)Py_None); - /* "cvcf.pyx":986 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":986 * def fetch(self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -19774,7 +20003,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p */ values[2] = ((PyObject *)Py_None); - /* "cvcf.pyx":987 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":987 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -19783,7 +20012,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p */ values[3] = ((PyObject *)Py_None); - /* "cvcf.pyx":988 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":988 * start = None, * end = None, * region = None ): # <<<<<<<<<<<<<< @@ -19836,7 +20065,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p __pyx_v_region = values[4]; } else { - /* "cvcf.pyx":985 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":985 * * def fetch(self, * reference = None, # <<<<<<<<<<<<<< @@ -19845,7 +20074,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p */ __pyx_v_reference = ((PyObject *)Py_None); - /* "cvcf.pyx":986 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":986 * def fetch(self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -19854,7 +20083,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p */ __pyx_v_start = ((PyObject *)Py_None); - /* "cvcf.pyx":987 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":987 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -19863,7 +20092,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p */ __pyx_v_end = ((PyObject *)Py_None); - /* "cvcf.pyx":988 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":988 * start = None, * end = None, * region = None ): # <<<<<<<<<<<<<< @@ -19890,7 +20119,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p return NULL; __pyx_L4_argument_unpacking_done:; - /* "cvcf.pyx":991 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":991 * """ Parse a stream of VCF-formatted lines. 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__pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, __pyx_t_1, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __pyx_t_5 = 0; @@ -19954,7 +20183,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p return __pyx_r; } -/* "cvcf.pyx":993 +/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":993 * return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) * * def validate( self, record ): # <<<<<<<<<<<<<< @@ -19962,10 +20191,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_40fetch(PyObject *__pyx_self, PyObject *__p * */ -static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_41validate[] = "validate vcf record.\n\n returns a validated record.\n "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_41validate = {__Pyx_NAMESTR("validate"), (PyCFunction)__pyx_pf_4cvcf_3VCF_41validate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_41validate)}; -static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_4cvcf_3VCF_validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4cvcf_3VCF_validate[] = "validate vcf record.\n\n returns a validated record.\n "; +static PyMethodDef __pyx_mdef_4cvcf_3VCF_validate = {__Pyx_NAMESTR("validate"), (PyCFunction)__pyx_pf_4cvcf_3VCF_validate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_validate)}; +static PyObject *__pyx_pf_4cvcf_3VCF_validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_record = 0; PyObject *__pyx_v_chrom; @@ -19990,6 +20219,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * int __pyx_v_movable; PyObject *__pyx_v_longest; PyObject *__pyx_v_shortest; + PyObject *__pyx_8genexpr1__pyx_v_allele; PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; @@ -20061,156 +20291,163 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * __pyx_v_faref_leftflank = Py_None; __Pyx_INCREF(Py_None); __pyx_v_faref = Py_None; __Pyx_INCREF(Py_None); __pyx_v_f = Py_None; __Pyx_INCREF(Py_None); - __pyx_v_newalts = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); + __pyx_v_newalts = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_v_a = Py_None; __Pyx_INCREF(Py_None); __pyx_v_l = Py_None; __Pyx_INCREF(Py_None); __pyx_v_addns = Py_None; __Pyx_INCREF(Py_None); __pyx_v_i = Py_None; __Pyx_INCREF(Py_None); __pyx_v_na = Py_None; __Pyx_INCREF(Py_None); __pyx_v_s = Py_None; __Pyx_INCREF(Py_None); - __pyx_v_alt = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); + __pyx_v_alt = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_v_addn = Py_None; __Pyx_INCREF(Py_None); __pyx_v_allele = Py_None; __Pyx_INCREF(Py_None); __pyx_v_longest = Py_None; __Pyx_INCREF(Py_None); __pyx_v_shortest = Py_None; __Pyx_INCREF(Py_None); + __pyx_8genexpr1__pyx_v_allele = Py_None; __Pyx_INCREF(Py_None); - /* "cvcf.pyx":999 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":999 * ''' * * raise NotImplementedError( "needs to be checked" ) # <<<<<<<<<<<<<< * * chrom, pos = record.chrom, record.pos */ 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":1001 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1001 * raise NotImplementedError( "needs to be checked" ) * * chrom, pos = record.chrom, record.pos # <<<<<<<<<<<<<< * * # check reference */ - __pyx_t_1 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__chrom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; 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= 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__match); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_10)); + __Pyx_GOTREF(__pyx_t_10); __Pyx_INCREF(__pyx_v_allele); PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_allele); __Pyx_GIVEREF(__pyx_v_allele); - __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_2, __pyx_t_10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 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- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_16 = __pyx_t_3; } else { __pyx_t_16 = __pyx_t_17; } if (__pyx_t_16) { - /* "cvcf.pyx":1098 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1098 * # left-align alleles, if a reference is available * if self._leftalign and self._reference: * while left < pos: # <<<<<<<<<<<<<< @@ -22098,13 +22352,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * * for allele in alt: */ while (1) { - __pyx_t_1 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); if (unlikely(!__pyx_t_1)) 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__pyx_t_13; __pyx_t_13 = 0; - goto __pyx_L72; + goto __pyx_L68; } /*else*/ { - /* "cvcf.pyx":1104 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1104 * longest, shortest = allele, ref * else: * longest, shortest = ref, allele # <<<<<<<<<<<<<< @@ -22182,9 +22437,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * __pyx_v_shortest = __pyx_t_5; __pyx_t_5 = 0; } - __pyx_L72:; + __pyx_L68:; - /* "cvcf.pyx":1105 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1105 * else: * longest, shortest = ref, allele * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): # <<<<<<<<<<<<<< @@ -22196,7 +22451,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * __pyx_t_16 = (__pyx_t_12 == __pyx_t_8); if (!__pyx_t_16) { __pyx_t_8 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_5 = 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (!__pyx_t_3) { @@ -22394,7 +22651,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * } if (__pyx_t_17) { - /* "cvcf.pyx":1114 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1114 * alt = [allele[:-1] for allele in alt] * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: * ref = faref_leftflank[pos-left-1] + ref # <<<<<<<<<<<<<< @@ -22403,32 +22660,33 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * */ __pyx_t_5 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 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goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - if (unlikely(__pyx_v_alt == Py_None)) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + if (likely(((PyObject *)__pyx_v_alt) != Py_None)) { + __pyx_t_6 = 0; __pyx_t_5 = ((PyObject *)__pyx_v_alt); __Pyx_INCREF(__pyx_t_5); + } else { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_6 = 0; __pyx_t_5 = ((PyObject *)__pyx_v_alt); __Pyx_INCREF(__pyx_t_5); for (;;) { if (__pyx_t_6 >= PyList_GET_SIZE(__pyx_t_5)) break; __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_6); __Pyx_INCREF(__pyx_t_4); __pyx_t_6++; @@ -22446,35 +22704,35 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * __pyx_t_13 = PyNumber_Add(__pyx_t_4, __pyx_v_allele); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_13); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_13))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_13))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; } __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __Pyx_INCREF(((PyObject *)__pyx_t_1)); + __Pyx_INCREF(((PyObject *)__pyx_t_2)); __Pyx_DECREF(((PyObject *)__pyx_v_alt)); - __pyx_v_alt = __pyx_t_1; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __pyx_v_alt = __pyx_t_2; + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - /* "cvcf.pyx":1116 + /* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":1116 * ref = faref_leftflank[pos-left-1] + ref * alt = [faref_leftflank[pos-left-1] + allele for allele in alt] * pos -= 1 # <<<<<<<<<<<<<< * * __all__ = [ */ - __pyx_t_1 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_pos); - __pyx_v_pos = __pyx_t_1; - __pyx_t_1 = 0; - goto __pyx_L78; + __pyx_v_pos = __pyx_t_2; + __pyx_t_2 = 0; + goto __pyx_L74; } - __pyx_L78:; + __pyx_L74:; } - __pyx_L69_break:; - goto __pyx_L67; + __pyx_L65_break:; + goto __pyx_L63; } - __pyx_L67:; + __pyx_L63:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -22513,6 +22771,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41validate(PyObject *__pyx_self, PyObject * __Pyx_DECREF(__pyx_v_allele); __Pyx_DECREF(__pyx_v_longest); __Pyx_DECREF(__pyx_v_shortest); + __Pyx_DECREF(__pyx_8genexpr1__pyx_v_allele); __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; @@ -22526,7 +22785,7 @@ static PyObject *__pyx_tp_new_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyOb 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_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_4cvcf_9VCFRecord___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -22686,7 +22945,7 @@ static PyNumberMethods __pyx_tp_as_number_VCFRecord = { }; static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = { - __pyx_pf_4cvcf_9VCFRecord_2__len__, /*sq_length*/ + __pyx_pf_4cvcf_9VCFRecord___len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_4cvcf_VCFRecord, /*sq_item*/ @@ -22699,8 +22958,8 @@ static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = { }; static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = { - __pyx_pf_4cvcf_9VCFRecord_2__len__, /*mp_length*/ - __pyx_pf_4cvcf_9VCFRecord_3__getitem__, /*mp_subscript*/ + __pyx_pf_4cvcf_9VCFRecord___len__, /*mp_length*/ + __pyx_pf_4cvcf_9VCFRecord___getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; @@ -22725,7 +22984,7 @@ static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = { #endif }; -static PyTypeObject __pyx_type_4cvcf_VCFRecord = { +PyTypeObject __pyx_type_4cvcf_VCFRecord = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cvcf.VCFRecord"), /*tp_name*/ sizeof(struct __pyx_obj_4cvcf_VCFRecord), /*tp_basicsize*/ @@ -22749,7 +23008,7 @@ static PyTypeObject __pyx_type_4cvcf_VCFRecord = { 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_VCFRecord, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 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*/ @@ -22922,7 +23181,7 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = { #endif }; -static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { +PyTypeObject __pyx_type_4cvcf_asVCFRecord = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cvcf.asVCFRecord"), /*tp_name*/ sizeof(struct __pyx_obj_4cvcf_asVCFRecord), /*tp_basicsize*/ @@ -22941,12 +23200,12 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { &__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/ 0, /*tp_hash*/ - __pyx_pf_4cvcf_11asVCFRecord_1__call__, /*tp_call*/ + __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_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 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*/ @@ -22979,6 +23238,8 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { }; 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} }; @@ -22998,107 +23259,124 @@ static struct PyModuleDef __pyx_moduledef = { static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 1, 0}, - {&__pyx_n_s_101, __pyx_k_101, sizeof(__pyx_k_101), 0, 0, 1, 1}, + {&__pyx_kp_s_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 1, 0}, + {&__pyx_kp_s_100, __pyx_k_100, sizeof(__pyx_k_100), 0, 0, 1, 0}, + {&__pyx_kp_s_101, __pyx_k_101, sizeof(__pyx_k_101), 0, 0, 1, 0}, {&__pyx_kp_s_102, __pyx_k_102, sizeof(__pyx_k_102), 0, 0, 1, 0}, {&__pyx_kp_s_103, __pyx_k_103, sizeof(__pyx_k_103), 0, 0, 1, 0}, - {&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0}, - {&__pyx_n_s_111, __pyx_k_111, sizeof(__pyx_k_111), 0, 0, 1, 1}, - {&__pyx_kp_s_112, __pyx_k_112, sizeof(__pyx_k_112), 0, 0, 1, 0}, - {&__pyx_n_s_113, __pyx_k_113, sizeof(__pyx_k_113), 0, 0, 1, 1}, - {&__pyx_kp_s_115, __pyx_k_115, sizeof(__pyx_k_115), 0, 0, 1, 0}, - 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- {&__pyx_kp_s_146, __pyx_k_146, sizeof(__pyx_k_146), 0, 0, 1, 0}, - {&__pyx_kp_s_147, __pyx_k_147, sizeof(__pyx_k_147), 0, 0, 1, 0}, - {&__pyx_kp_s_148, __pyx_k_148, sizeof(__pyx_k_148), 0, 0, 1, 0}, - {&__pyx_kp_s_149, __pyx_k_149, sizeof(__pyx_k_149), 0, 0, 1, 0}, - {&__pyx_kp_s_150, __pyx_k_150, sizeof(__pyx_k_150), 0, 0, 1, 0}, - {&__pyx_kp_s_151, __pyx_k_151, sizeof(__pyx_k_151), 0, 0, 1, 0}, - {&__pyx_kp_s_152, __pyx_k_152, sizeof(__pyx_k_152), 0, 0, 1, 0}, - {&__pyx_kp_s_153, __pyx_k_153, sizeof(__pyx_k_153), 0, 0, 1, 0}, - {&__pyx_kp_s_154, __pyx_k_154, sizeof(__pyx_k_154), 0, 0, 1, 0}, - {&__pyx_kp_s_155, __pyx_k_155, sizeof(__pyx_k_155), 0, 0, 1, 0}, - {&__pyx_kp_s_156, __pyx_k_156, sizeof(__pyx_k_156), 0, 0, 1, 0}, - {&__pyx_kp_s_157, __pyx_k_157, sizeof(__pyx_k_157), 0, 0, 1, 0}, - {&__pyx_kp_s_158, __pyx_k_158, sizeof(__pyx_k_158), 0, 0, 1, 0}, - {&__pyx_kp_s_159, __pyx_k_159, sizeof(__pyx_k_159), 0, 0, 1, 0}, - {&__pyx_kp_s_160, __pyx_k_160, sizeof(__pyx_k_160), 0, 0, 1, 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sizeof(__pyx_k_26), 0, 0, 1, 1}, {&__pyx_kp_s_27, __pyx_k_27, sizeof(__pyx_k_27), 0, 0, 1, 0}, - {&__pyx_n_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 1}, + {&__pyx_kp_s_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 1, 0}, + {&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0}, + {&__pyx_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0}, {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0}, + {&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0}, + {&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0}, {&__pyx_kp_s_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 1, 0}, - {&__pyx_n_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 1}, - {&__pyx_n_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 1}, + {&__pyx_kp_s_35, __pyx_k_35, sizeof(__pyx_k_35), 0, 0, 1, 0}, + {&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0}, + {&__pyx_kp_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 0}, {&__pyx_kp_s_4, __pyx_k_4, sizeof(__pyx_k_4), 0, 0, 1, 0}, {&__pyx_kp_s_40, __pyx_k_40, sizeof(__pyx_k_40), 0, 0, 1, 0}, {&__pyx_kp_s_41, __pyx_k_41, sizeof(__pyx_k_41), 0, 0, 1, 0}, {&__pyx_kp_s_42, __pyx_k_42, sizeof(__pyx_k_42), 0, 0, 1, 0}, {&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0}, + {&__pyx_kp_s_44, __pyx_k_44, sizeof(__pyx_k_44), 0, 0, 1, 0}, + {&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0}, + {&__pyx_kp_s_46, __pyx_k_46, sizeof(__pyx_k_46), 0, 0, 1, 0}, + {&__pyx_n_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 1}, + {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0}, + {&__pyx_kp_s_49, __pyx_k_49, sizeof(__pyx_k_49), 0, 0, 1, 0}, + {&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0}, + {&__pyx_kp_s_50, __pyx_k_50, sizeof(__pyx_k_50), 0, 0, 1, 0}, + {&__pyx_kp_s_51, __pyx_k_51, sizeof(__pyx_k_51), 0, 0, 1, 0}, {&__pyx_n_s_52, __pyx_k_52, sizeof(__pyx_k_52), 0, 0, 1, 1}, - {&__pyx_kp_s_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 0}, + {&__pyx_kp_s_53, __pyx_k_53, sizeof(__pyx_k_53), 0, 0, 1, 0}, + {&__pyx_kp_s_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 0}, + {&__pyx_n_s_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 1}, {&__pyx_kp_s_56, __pyx_k_56, sizeof(__pyx_k_56), 0, 0, 1, 0}, {&__pyx_kp_s_57, __pyx_k_57, sizeof(__pyx_k_57), 0, 0, 1, 0}, - {&__pyx_kp_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 0}, - {&__pyx_kp_s_59, __pyx_k_59, sizeof(__pyx_k_59), 0, 0, 1, 0}, + {&__pyx_n_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 1}, + {&__pyx_n_s_59, __pyx_k_59, sizeof(__pyx_k_59), 0, 0, 1, 1}, + {&__pyx_kp_b_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 0, 0}, {&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0}, - {&__pyx_kp_s_61, __pyx_k_61, sizeof(__pyx_k_61), 0, 0, 1, 0}, - {&__pyx_kp_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 0}, + {&__pyx_n_s_60, __pyx_k_60, sizeof(__pyx_k_60), 0, 0, 1, 1}, + {&__pyx_n_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 1}, {&__pyx_kp_s_63, __pyx_k_63, sizeof(__pyx_k_63), 0, 0, 1, 0}, + {&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0}, + {&__pyx_n_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 1}, {&__pyx_kp_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 0}, - {&__pyx_kp_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 0}, + {&__pyx_n_s_67, __pyx_k_67, sizeof(__pyx_k_67), 0, 0, 1, 1}, + {&__pyx_kp_s_68, __pyx_k_68, sizeof(__pyx_k_68), 0, 0, 1, 0}, + {&__pyx_n_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 1}, + {&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0}, {&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0}, {&__pyx_kp_s_71, __pyx_k_71, sizeof(__pyx_k_71), 0, 0, 1, 0}, {&__pyx_kp_s_72, __pyx_k_72, sizeof(__pyx_k_72), 0, 0, 1, 0}, {&__pyx_kp_s_73, __pyx_k_73, sizeof(__pyx_k_73), 0, 0, 1, 0}, + {&__pyx_kp_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 0}, + {&__pyx_kp_s_75, __pyx_k_75, sizeof(__pyx_k_75), 0, 0, 1, 0}, {&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0}, {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0}, {&__pyx_kp_s_78, __pyx_k_78, sizeof(__pyx_k_78), 0, 0, 1, 0}, - {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1}, + {&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0}, {&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0}, {&__pyx_kp_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 0}, {&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0}, {&__pyx_kp_s_82, __pyx_k_82, sizeof(__pyx_k_82), 0, 0, 1, 0}, + {&__pyx_kp_s_83, __pyx_k_83, sizeof(__pyx_k_83), 0, 0, 1, 0}, + {&__pyx_kp_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 0}, {&__pyx_kp_s_85, __pyx_k_85, sizeof(__pyx_k_85), 0, 0, 1, 0}, - {&__pyx_n_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 1}, + {&__pyx_kp_s_86, __pyx_k_86, sizeof(__pyx_k_86), 0, 0, 1, 0}, + {&__pyx_kp_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 0}, {&__pyx_kp_s_88, __pyx_k_88, sizeof(__pyx_k_88), 0, 0, 1, 0}, {&__pyx_kp_s_89, __pyx_k_89, sizeof(__pyx_k_89), 0, 0, 1, 0}, - {&__pyx_kp_b_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 0, 0}, - {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 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(unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_6 = PyInt_FromLong(6); if (unlikely(!__pyx_int_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_7 = PyInt_FromLong(7); if (unlikely(!__pyx_int_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_9 = PyInt_FromLong(9); if (unlikely(!__pyx_int_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_10 = PyInt_FromLong(10); if (unlikely(!__pyx_int_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_11 = PyInt_FromLong(11); if (unlikely(!__pyx_int_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __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;}; + __pyx_int_13 = PyInt_FromLong(13); if (unlikely(!__pyx_int_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __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;}; + __pyx_int_19 = PyInt_FromLong(19); if (unlikely(!__pyx_int_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_20 = PyInt_FromLong(20); if (unlikely(!__pyx_int_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_21 = PyInt_FromLong(21); if (unlikely(!__pyx_int_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_22 = PyInt_FromLong(22); if (unlikely(!__pyx_int_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_23 = PyInt_FromLong(23); if (unlikely(!__pyx_int_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_24 = PyInt_FromLong(24); if (unlikely(!__pyx_int_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_int_25 = PyInt_FromLong(25); if (unlikely(!__pyx_int_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = 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__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; - /* "ctabix.pxd":2 + /* "pysam/ctabix.pxd":2 * * cdef extern from "string.h": # <<<<<<<<<<<<<< * ctypedef int size_t @@ -25287,6 +25113,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) __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; @@ -25312,6 +25139,19 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *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, @@ -25342,19 +25182,6 @@ static void __Pyx_RaiseArgtupleInvalid( func_name, more_or_less, num_expected, number, num_found); } -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 int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], @@ -25413,210 +25240,73 @@ static int __Pyx_ParseOptionalKeywords( } } } - 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 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 , */ - 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; + 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; } -#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"); +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 (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"); + #if PY_MAJOR_VERSION >= 3 + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) 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); - } - } - + #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: - return; + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; } -#endif + static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; @@ -25756,91 +25446,167 @@ bad: return module; } -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 PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, - PyObject *modname) { - PyObject *result; - PyObject *metaclass; - - if (PyDict_SetItemString(dict, "__module__", modname) < 0) - return NULL; +static PyObject *__Pyx_CreateClass( + PyObject *bases, PyObject *dict, PyObject *name, const char *modname) +{ + PyObject *py_modname; + PyObject *result = 0; - /* Python2 __metaclass__ */ - metaclass = PyDict_GetItemString(dict, "__metaclass__"); - if (metaclass) { - Py_INCREF(metaclass); - } else { - metaclass = __Pyx_FindPy2Metaclass(bases); - } - result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL); - Py_DECREF(metaclass); + #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(); -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; + 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 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); +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_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) { - if (obj == Py_None) - obj = NULL; - return PyMethod_New(func, obj, type); + +#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 , */ + 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; } -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; +#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; } - __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type; - return 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; + } + + 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; @@ -26295,13 +26061,13 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class 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 @@ -26311,7 +26077,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #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; @@ -26346,23 +26112,22 @@ bad: } #endif -static void* __Pyx_GetVtable(PyObject *dict) { - void* ptr; +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) - ptr = PyCapsule_GetPointer(ob, 0); + *(void **)vtabptr = PyCapsule_GetPointer(ob, 0); #else - ptr = PyCObject_AsVoidPtr(ob); + *(void **)vtabptr = PyCObject_AsVoidPtr(ob); #endif - if (!ptr && !PyErr_Occurred()) - PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type"); + if (!*(void **)vtabptr) + goto bad; Py_DECREF(ob); - return ptr; + return 0; bad: Py_XDECREF(ob); - return NULL; + return -1; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) {