-/* Generated by Cython 0.13 on Thu May 5 14:57:52 2011 */
+/* Generated by Cython 0.14.1 on Thu Nov 17 22:34:01 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "stdio.h"
#include "pythread.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
static const char *__pyx_f[] = {
"TabProxies.pyx",
"bool.pxd",
+ "complex.pxd",
};
/* Type declarations */
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":78
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":92
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":61
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":81
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
};
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":20
+/* "TabProxies.pyx":20
* return not (buffer <= p < buffer + nbytes )
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":488
+/* "TabProxies.pyx":493
* self.fromDict( r )
*
* cdef class NamedTupleProxy( TupleProxy ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":573
+/* "TabProxies.pyx":578
* TupleProxy._setindex(self, idx, str(value) )
*
* cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":507
+/* "TabProxies.pyx":512
* return f( self.fields[idx] )
*
* cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":231
+/* "TabProxies.pyx":240
* return str(v)
*
* cdef class GTFProxy( TupleProxy ): # <<<<<<<<<<<<<<
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name, PyObject* kw_name); /*proto*/
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
-static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
-static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
/* Module declarations from cpython.float */
+/* Module declarations from __builtin__ */
+
/* Module declarations from cpython.complex */
+static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from cpython.string */
/* Module declarations from cpython.unicode */
static char *__pyx_f_10TabProxies_StrOrEmpty(char *); /*proto*/
static int __pyx_f_10TabProxies_isNew(char *, char *, size_t); /*proto*/
#define __Pyx_MODULE_NAME "TabProxies"
-int __pyx_module_is_main_TabProxies = 0;
+static int __pyx_module_is_main_TabProxies = 0;
/* Implementation of TabProxies */
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IndexError;
+static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_xrange;
static PyObject *__pyx_builtin_TypeError;
static char __pyx_k_1[] = "malformatted entry at %s";
static char __pyx_k_2[] = "";
static char __pyx_k_3[] = "out of memory";
-static char __pyx_k_4[] = "incomplete line at %s";
-static char __pyx_k_5[] = "row too large - more than %i fields";
-static char __pyx_k_6[] = "list index out of range";
-static char __pyx_k_7[] = "\t";
-static char __pyx_k_8[] = ".";
-static char __pyx_k_9[] = "\"%s\"";
-static char __pyx_k_10[] = ";";
-static char __pyx_k_11[] = " ";
-static char __pyx_k_12[] = "\"";
-static char __pyx_k_13[] = "%s \"%s\"";
-static char __pyx_k_14[] = "%s %s";
-static char __pyx_k_15[] = "; ";
-static char __pyx_k_16[] = "'GTFProxy' has no attribute '%s'";
-static char __pyx_k_17[] = "field %s not set";
-static char __pyx_k_18[] = "bed format requires at least three columns";
-static char __pyx_k_19[] = "contig of feature.";
-static char __pyx_k_20[] = "feature name.";
-static char __pyx_k_21[] = "feature source.";
-static char __pyx_k_22[] = "feature start (in 0-based open/closed coordinates).";
-static char __pyx_k_23[] = "feature end (in 0-based open/closed coordinates).";
-static char __pyx_k_24[] = "feature score.";
-static char __pyx_k_25[] = "feature strand.";
-static char __pyx_k_26[] = "feature frame.";
-static char __pyx_k_27[] = "feature attributes (as a string).";
-static char __pyx_k_28[] = "TupleProxy._setindex (line 154)";
-static char __pyx_k_29[] = "TupleProxy.__setitem__ (line 177)";
-static char __pyx_k_30[] = "TupleProxy.__next__ (line 192)";
-static char __pyx_k_31[] = "TupleProxy.__str__ (line 202)";
-static char __pyx_k_32[] = "toDot (line 219)";
-static char __pyx_k_33[] = "quote (line 224)";
-static char __pyx_k_34[] = "GTFProxy.asDict (line 350)";
-static char __pyx_k_35[] = "GTFProxy.fromDict (line 385)";
-static char __pyx_k_36[] = "GTFProxy.invert (line 430)";
-static char __pyx_k_37[] = "GTFProxy.keys (line 441)";
-static char __pyx_k_38[] = "GTFProxy.__getattr__ (line 449)";
-static char __pyx_k_39[] = "GTFProxy.setAttribute (line 482)";
-static char __pyx_k_40[] = "NamedTupleProxy.__setattr__ (line 492)";
-static char __pyx_k_41[] = "BedProxy.__setattr__ (line 564)";
-static char __pyx_k_42[] = "VCFProxy.__setattr__ (line 608)";
+static char __pyx_k_5[] = "incomplete line at %s";
+static char __pyx_k_7[] = "row too large - more than %i fields";
+static char __pyx_k_8[] = "list index out of range";
+static char __pyx_k_10[] = "list index out of range %i >= %i";
+static char __pyx_k_14[] = "\t";
+static char __pyx_k_16[] = ".";
+static char __pyx_k_17[] = "\"%s\"";
+static char __pyx_k_18[] = ";";
+static char __pyx_k_20[] = " ";
+static char __pyx_k_22[] = "\"";
+static char __pyx_k_23[] = "%s \"%s\"";
+static char __pyx_k_24[] = "%s %s";
+static char __pyx_k_25[] = "; ";
+static char __pyx_k_29[] = "'GTFProxy' has no attribute '%s'";
+static char __pyx_k_30[] = "field %s not set";
+static char __pyx_k_31[] = "bed format requires at least three columns";
+static char __pyx_k_33[] = "contig of feature.";
+static char __pyx_k_34[] = "feature name.";
+static char __pyx_k_35[] = "feature source.";
+static char __pyx_k_36[] = "feature start (in 0-based open/closed coordinates).";
+static char __pyx_k_37[] = "feature end (in 0-based open/closed coordinates).";
+static char __pyx_k_38[] = "feature score.";
+static char __pyx_k_39[] = "feature strand.";
+static char __pyx_k_40[] = "feature frame.";
+static char __pyx_k_41[] = "feature attributes (as a string).";
static char __pyx_k__id[] = "id";
static char __pyx_k__alt[] = "alt";
static char __pyx_k__end[] = "end";
static char __pyx_k__data[] = "data";
static char __pyx_k__info[] = "info";
static char __pyx_k__join[] = "join";
-static char __pyx_k__keys[] = "keys";
static char __pyx_k__name[] = "name";
static char __pyx_k__qual[] = "qual";
static char __pyx_k__frame[] = "frame";
static char __pyx_k__toDot[] = "toDot";
static char __pyx_k__types[] = "types";
static char __pyx_k__value[] = "value";
+static char __pyx_k__append[] = "append";
static char __pyx_k__asDict[] = "asDict";
static char __pyx_k__contig[] = "contig";
static char __pyx_k__fields[] = "fields";
static char __pyx_k__filter[] = "filter";
static char __pyx_k__format[] = "format";
-static char __pyx_k__invert[] = "invert";
static char __pyx_k__nbytes[] = "nbytes";
static char __pyx_k__offset[] = "offset";
static char __pyx_k__source[] = "source";
static char __pyx_k__xrange[] = "xrange";
static char __pyx_k____str__[] = "__str__";
static char __pyx_k__feature[] = "feature";
+static char __pyx_k__indices[] = "indices";
static char __pyx_k__itemRGB[] = "itemRGB";
static char __pyx_k__nfields[] = "nfields";
-static char __pyx_k__BedProxy[] = "BedProxy";
-static char __pyx_k__GTFProxy[] = "GTFProxy";
static char __pyx_k__KeyError[] = "KeyError";
-static char __pyx_k__VCFProxy[] = "VCFProxy";
static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__fromDict[] = "fromDict";
static char __pyx_k__thickEnd[] = "thickEnd";
static char __pyx_k__TypeError[] = "TypeError";
+static char __pyx_k___getindex[] = "_getindex";
static char __pyx_k___setindex[] = "_setindex";
static char __pyx_k__bedfields[] = "bedfields";
static char __pyx_k__IndexError[] = "IndexError";
static char __pyx_k__StringType[] = "StringType";
-static char __pyx_k__TupleProxy[] = "TupleProxy";
+static char __pyx_k__TabProxies[] = "TabProxies";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k__attributes[] = "attributes";
static char __pyx_k__blockCount[] = "blockCount";
static char __pyx_k__thickStart[] = "thickStart";
static char __pyx_k__StringTypes[] = "StringTypes";
static char __pyx_k____getattr__[] = "__getattr__";
-static char __pyx_k____setattr__[] = "__setattr__";
static char __pyx_k____setitem__[] = "__setitem__";
static char __pyx_k__blockStarts[] = "blockStarts";
static char __pyx_k__is_modified[] = "is_modified";
static char __pyx_k__getMaxFields[] = "getMaxFields";
-static char __pyx_k__setAttribute[] = "setAttribute";
static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__map_key2field[] = "map_key2field";
static char __pyx_k__AttributeError[] = "AttributeError";
-static char __pyx_k__NamedTupleProxy[] = "NamedTupleProxy";
static char __pyx_k__hasOwnAttributes[] = "hasOwnAttributes";
static PyObject *__pyx_kp_s_1;
static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_11;
-static PyObject *__pyx_kp_s_12;
-static PyObject *__pyx_kp_s_13;
static PyObject *__pyx_kp_s_14;
-static PyObject *__pyx_kp_s_15;
static PyObject *__pyx_kp_s_16;
static PyObject *__pyx_kp_s_17;
static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_2;
-static PyObject *__pyx_kp_u_28;
-static PyObject *__pyx_kp_u_29;
+static PyObject *__pyx_kp_s_20;
+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_kp_s_29;
static PyObject *__pyx_kp_s_3;
-static PyObject *__pyx_kp_u_30;
-static PyObject *__pyx_kp_u_31;
-static PyObject *__pyx_kp_u_32;
-static PyObject *__pyx_kp_u_33;
-static PyObject *__pyx_kp_u_34;
-static PyObject *__pyx_kp_u_35;
-static PyObject *__pyx_kp_u_36;
-static PyObject *__pyx_kp_u_37;
-static PyObject *__pyx_kp_u_38;
-static PyObject *__pyx_kp_u_39;
-static PyObject *__pyx_kp_s_4;
-static PyObject *__pyx_kp_u_40;
-static PyObject *__pyx_kp_u_41;
-static PyObject *__pyx_kp_u_42;
+static PyObject *__pyx_kp_s_30;
+static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_8;
-static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__AttributeError;
-static PyObject *__pyx_n_s__BedProxy;
-static PyObject *__pyx_n_s__GTFProxy;
static PyObject *__pyx_n_s__IndexError;
static PyObject *__pyx_n_s__KeyError;
-static PyObject *__pyx_n_s__NamedTupleProxy;
static PyObject *__pyx_n_s__StopIteration;
static PyObject *__pyx_n_s__StringType;
static PyObject *__pyx_n_s__StringTypes;
-static PyObject *__pyx_n_s__TupleProxy;
+static PyObject *__pyx_n_s__TabProxies;
static PyObject *__pyx_n_s__TypeError;
-static PyObject *__pyx_n_s__VCFProxy;
static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____getattr__;
static PyObject *__pyx_n_s____main__;
-static PyObject *__pyx_n_s____next__;
-static PyObject *__pyx_n_s____setattr__;
static PyObject *__pyx_n_s____setitem__;
static PyObject *__pyx_n_s____str__;
static PyObject *__pyx_n_s____test__;
+static PyObject *__pyx_n_s___getindex;
static PyObject *__pyx_n_s___setindex;
static PyObject *__pyx_n_s__alt;
+static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__asDict;
static PyObject *__pyx_n_s__attributes;
static PyObject *__pyx_n_s__bedfields;
static PyObject *__pyx_n_s__hasOwnAttributes;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__index;
+static PyObject *__pyx_n_s__indices;
static PyObject *__pyx_n_s__info;
-static PyObject *__pyx_n_s__invert;
static PyObject *__pyx_n_s__is_modified;
static PyObject *__pyx_n_s__itemRGB;
static PyObject *__pyx_n_s__items;
static PyObject *__pyx_n_s__join;
-static PyObject *__pyx_n_s__keys;
static PyObject *__pyx_n_s__map_key2field;
static PyObject *__pyx_n_s__name;
static PyObject *__pyx_n_s__nbytes;
static PyObject *__pyx_n_s__range;
static PyObject *__pyx_n_s__ref;
static PyObject *__pyx_n_s__score;
-static PyObject *__pyx_n_s__setAttribute;
static PyObject *__pyx_n_s__source;
static PyObject *__pyx_n_s__split;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_int_9;
static PyObject *__pyx_int_10;
static PyObject *__pyx_int_11;
-
-/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":4
+static PyObject *__pyx_k_tuple_4;
+static PyObject *__pyx_k_tuple_6;
+static PyObject *__pyx_k_tuple_9;
+static PyObject *__pyx_k_tuple_11;
+static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_13;
+static PyObject *__pyx_k_tuple_15;
+static PyObject *__pyx_k_tuple_19;
+static PyObject *__pyx_k_tuple_21;
+static PyObject *__pyx_k_tuple_26;
+static PyObject *__pyx_k_tuple_27;
+static PyObject *__pyx_k_tuple_28;
+static PyObject *__pyx_k_tuple_32;
+
+/* "TabProxies.pyx":4
* from cpython cimport PyString_FromStringAndSize, PyString_AsString, PyString_AS_STRING
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#endif
};
-PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
+static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.TupleProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_TupleProxy), /*tp_basicsize*/
&__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_10TabProxies_10TupleProxy___str__, /*tp_str*/
+ __pyx_pf_10TabProxies_10TupleProxy_9__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_TupleProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to parsed row as a tuple.\n\n This class represents a table row for fast read-access.\n\n Access to individual fields is via the [] operator.\n \n Only read-only access is implemented.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_10TabProxies_10TupleProxy___iter__, /*tp_iter*/
- __pyx_pf_10TabProxies_10TupleProxy___next__, /*tp_iternext*/
+ __pyx_pf_10TabProxies_10TupleProxy_7__iter__, /*tp_iter*/
+ __pyx_pf_10TabProxies_10TupleProxy_8__next__, /*tp_iternext*/
__pyx_methods_10TabProxies_TupleProxy, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_10TabProxies_8GTFProxy___dealloc__(o);
+ __pyx_pf_10TabProxies_8GTFProxy_1__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
PyObject *v = PyObject_GenericGetAttr(o, n);
if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Clear();
- v = __pyx_pf_10TabProxies_8GTFProxy___getattr__(o, n);
+ v = __pyx_pf_10TabProxies_8GTFProxy_8__getattr__(o, n);
}
return v;
}
static int __pyx_setprop_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_6contig___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_6contig_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_7feature___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_7feature_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_6source___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_6source_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_5start___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_5start_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_3end___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_3end_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_5score___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_5score_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_6strand___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_6strand_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_5frame___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_5frame_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
static int __pyx_setprop_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pf_10TabProxies_8GTFProxy_10attributes___set__(o, v);
+ return __pyx_pf_10TabProxies_8GTFProxy_10attributes_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
static PyMethodDef __pyx_methods_10TabProxies_GTFProxy[] = {
- {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_asDict)},
- {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_fromDict)},
- {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_invert, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_invert)},
- {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_keys)},
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy___getattr__)},
- {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_setAttribute)},
+ {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_2asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_2asDict)},
+ {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_3fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_3fromDict)},
+ {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_5invert, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_5invert)},
+ {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_6keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_6keys)},
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_8__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_8__getattr__)},
+ {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_9setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_9setAttribute)},
{0, 0, 0, 0}
};
static struct PyGetSetDef __pyx_getsets_10TabProxies_GTFProxy[] = {
- {(char *)"contig", __pyx_getprop_10TabProxies_8GTFProxy_contig, __pyx_setprop_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_19), 0},
- {(char *)"feature", __pyx_getprop_10TabProxies_8GTFProxy_feature, __pyx_setprop_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_20), 0},
- {(char *)"source", __pyx_getprop_10TabProxies_8GTFProxy_source, __pyx_setprop_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_21), 0},
- {(char *)"start", __pyx_getprop_10TabProxies_8GTFProxy_start, __pyx_setprop_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_22), 0},
- {(char *)"end", __pyx_getprop_10TabProxies_8GTFProxy_end, __pyx_setprop_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_23), 0},
- {(char *)"score", __pyx_getprop_10TabProxies_8GTFProxy_score, __pyx_setprop_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_24), 0},
- {(char *)"strand", __pyx_getprop_10TabProxies_8GTFProxy_strand, __pyx_setprop_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_25), 0},
- {(char *)"frame", __pyx_getprop_10TabProxies_8GTFProxy_frame, __pyx_setprop_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_26), 0},
- {(char *)"attributes", __pyx_getprop_10TabProxies_8GTFProxy_attributes, __pyx_setprop_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_27), 0},
+ {(char *)"contig", __pyx_getprop_10TabProxies_8GTFProxy_contig, __pyx_setprop_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_33), 0},
+ {(char *)"feature", __pyx_getprop_10TabProxies_8GTFProxy_feature, __pyx_setprop_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_34), 0},
+ {(char *)"source", __pyx_getprop_10TabProxies_8GTFProxy_source, __pyx_setprop_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_35), 0},
+ {(char *)"start", __pyx_getprop_10TabProxies_8GTFProxy_start, __pyx_setprop_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_36), 0},
+ {(char *)"end", __pyx_getprop_10TabProxies_8GTFProxy_end, __pyx_setprop_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_37), 0},
+ {(char *)"score", __pyx_getprop_10TabProxies_8GTFProxy_score, __pyx_setprop_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_38), 0},
+ {(char *)"strand", __pyx_getprop_10TabProxies_8GTFProxy_strand, __pyx_setprop_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_39), 0},
+ {(char *)"frame", __pyx_getprop_10TabProxies_8GTFProxy_frame, __pyx_setprop_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_40), 0},
+ {(char *)"attributes", __pyx_getprop_10TabProxies_8GTFProxy_attributes, __pyx_setprop_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_41), 0},
{0, 0, 0, 0, 0}
};
static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = {
0, /*mp_length*/
- __pyx_pf_10TabProxies_8GTFProxy___getitem__, /*mp_subscript*/
+ __pyx_pf_10TabProxies_8GTFProxy_7__getitem__, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
+static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.GTFProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_GTFProxy), /*tp_basicsize*/
&__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_10TabProxies_8GTFProxy___str__, /*tp_str*/
+ __pyx_pf_10TabProxies_8GTFProxy_4__str__, /*tp_str*/
__pyx_tp_getattro_10TabProxies_GTFProxy, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_GTFProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to GTF fields.\n\n This class represents a GTF entry for fast read-access.\n Write-access has been added as well, though some care must\n be taken. If any of the string fields (contig, source, ...)\n are set, the new value is tied to the lifetime of the\n argument that was supplied.\n\n The only exception is the attributes field when set from\n a dictionary - this field will manage its own memory.\n\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
PyObject *v = PyObject_GenericGetAttr(o, n);
if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Clear();
- v = __pyx_pf_10TabProxies_15NamedTupleProxy___getattr__(o, n);
+ v = __pyx_pf_10TabProxies_15NamedTupleProxy_1__getattr__(o, n);
}
return v;
}
}
static PyMethodDef __pyx_methods_10TabProxies_NamedTupleProxy[] = {
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_15NamedTupleProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_15NamedTupleProxy_1__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
+static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.NamedTupleProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), /*tp_basicsize*/
__pyx_tp_getattro_10TabProxies_NamedTupleProxy, /*tp_getattro*/
__pyx_tp_setattro_10TabProxies_NamedTupleProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_NamedTupleProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
0, /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
static int __pyx_tp_setattro_10TabProxies_BedProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pf_10TabProxies_8BedProxy___setattr__(o, n, v);
+ return __pyx_pf_10TabProxies_8BedProxy_1__setattr__(o, n, v);
}
else {
if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
#endif
};
-PyTypeObject __pyx_type_10TabProxies_BedProxy = {
+static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.BedProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_BedProxy), /*tp_basicsize*/
0, /*tp_getattro*/
__pyx_tp_setattro_10TabProxies_BedProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_BedProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to Bed fields.\n\n This class represents a GTF entry for fast read-access.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
static int __pyx_tp_setattro_10TabProxies_VCFProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pf_10TabProxies_8VCFProxy___setattr__(o, n, v);
+ return __pyx_pf_10TabProxies_8VCFProxy_2__setattr__(o, n, v);
}
else {
if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
}
}
+static PyObject *__pyx_getprop_10TabProxies_8VCFProxy_pos(PyObject *o, void *x) {
+ return __pyx_pf_10TabProxies_8VCFProxy_3pos___get__(o);
+}
+
static PyMethodDef __pyx_methods_10TabProxies_VCFProxy[] = {
{0, 0, 0, 0}
};
+static struct PyGetSetDef __pyx_getsets_10TabProxies_VCFProxy[] = {
+ {(char *)"pos", __pyx_getprop_10TabProxies_8VCFProxy_pos, 0, __Pyx_DOCSTR(__pyx_k_37), 0},
+ {0, 0, 0, 0, 0}
+};
+
static PyNumberMethods __pyx_tp_as_number_VCFProxy = {
0, /*nb_add*/
0, /*nb_subtract*/
};
static PySequenceMethods __pyx_tp_as_sequence_VCFProxy = {
- __pyx_pf_10TabProxies_8VCFProxy___len__, /*sq_length*/
+ __pyx_pf_10TabProxies_8VCFProxy_1__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
};
static PyMappingMethods __pyx_tp_as_mapping_VCFProxy = {
- __pyx_pf_10TabProxies_8VCFProxy___len__, /*mp_length*/
+ __pyx_pf_10TabProxies_8VCFProxy_1__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
#endif
};
-PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
+static PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("TabProxies.VCFProxy"), /*tp_name*/
sizeof(struct __pyx_obj_10TabProxies_VCFProxy), /*tp_basicsize*/
0, /*tp_getattro*/
__pyx_tp_setattro_10TabProxies_VCFProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_VCFProxy, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to VCF fields.\n\n The genotypes are accessed via index.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_iternext*/
__pyx_methods_10TabProxies_VCFProxy, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_10TabProxies_VCFProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
};
static PyMethodDef __pyx_methods[] = {
- {__Pyx_NAMESTR("toDot"), (PyCFunction)__pyx_pf_10TabProxies_toDot, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_toDot)},
- {__Pyx_NAMESTR("quote"), (PyCFunction)__pyx_pf_10TabProxies_quote, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_quote)},
{0, 0, 0, 0}
};
static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 1, 0},
{&__pyx_kp_s_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 1, 0},
- {&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0},
- {&__pyx_kp_s_12, __pyx_k_12, sizeof(__pyx_k_12), 0, 0, 1, 0},
- {&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
{&__pyx_kp_s_14, __pyx_k_14, sizeof(__pyx_k_14), 0, 0, 1, 0},
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{&__pyx_kp_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 0},
{&__pyx_kp_s_17, __pyx_k_17, sizeof(__pyx_k_17), 0, 0, 1, 0},
{&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
{&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
- {&__pyx_kp_u_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 1, 0, 0},
- {&__pyx_kp_u_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 1, 0, 0},
+ {&__pyx_kp_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 0},
+ {&__pyx_kp_s_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 1, 0},
+ {&__pyx_kp_s_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 1, 0},
+ {&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
+ {&__pyx_kp_s_25, __pyx_k_25, sizeof(__pyx_k_25), 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_u_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 1, 0, 0},
- {&__pyx_kp_u_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 1, 0, 0},
- {&__pyx_kp_u_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 1, 0, 0},
- {&__pyx_kp_u_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 1, 0, 0},
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+ * raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
+ * memcpy( self.attributes, p, l )
+ *
+ */
+ __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_26));
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_3));
+ PyTuple_SET_ITEM(__pyx_k_tuple_26, 0, ((PyObject *)__pyx_kp_s_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
+
+ /* "TabProxies.pyx":454
+ * '''return a list of attributes defined in this entry.'''
+ * r = self.attributes
+ * return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ] # <<<<<<<<<<<<<<
+ *
+ * def __getitem__(self, key):
+ */
+ __pyx_k_tuple_27 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_27));
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_18));
+ PyTuple_SET_ITEM(__pyx_k_tuple_27, 0, ((PyObject *)__pyx_kp_s_18));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_18));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_27));
+ __pyx_k_tuple_28 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_28));
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_20));
+ PyTuple_SET_ITEM(__pyx_k_tuple_28, 0, ((PyObject *)__pyx_kp_s_20));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_20));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_28));
+
+ /* "TabProxies.pyx":543
+ *
+ * if self.nfields < 3:
+ * raise ValueError( "bed format requires at least three columns" ) # <<<<<<<<<<<<<<
+ *
+ * # determines bed format
+ */
+ __pyx_k_tuple_32 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_32));
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_31));
+ PyTuple_SET_ITEM(__pyx_k_tuple_32, 0, ((PyObject *)__pyx_kp_s_31));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_31));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_32));
+ __Pyx_RefNannyFinishContext();
+ return 0;
+ __pyx_L1_error:;
+ __Pyx_RefNannyFinishContext();
+ return -1;
+}
+
+static int __Pyx_InitGlobals(void) {
+ if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_2 = PyInt_FromLong(2); if (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_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;};
+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
+
+#if PY_MAJOR_VERSION < 3
+PyMODINIT_FUNC initTabProxies(void); /*proto*/
PyMODINIT_FUNC initTabProxies(void)
#else
PyMODINIT_FUNC PyInit_TabProxies(void); /*proto*/
{
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
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void* __pyx_refnanny = NULL;
__Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
}
/*--- Builtin init code ---*/
if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Constants init code ---*/
+ if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
__pyx_vtabptr_10TabProxies_TupleProxy = &__pyx_vtable_10TabProxies_TupleProxy;
- #if PY_MAJOR_VERSION >= 3
__pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
__pyx_vtable_10TabProxies_TupleProxy.take = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_take;
__pyx_vtable_10TabProxies_TupleProxy.present = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_present;
__pyx_vtable_10TabProxies_TupleProxy.copy = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_copy;
__pyx_vtable_10TabProxies_TupleProxy.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.take = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_take;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.present = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_present;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.copy = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_copy;
- *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.update = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_update;
- #endif
if (PyType_Ready(&__pyx_type_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__setitem__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__.doc = __pyx_doc_10TabProxies_10TupleProxy___setitem__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_5__setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_5__setitem__.doc = __pyx_doc_10TabProxies_10TupleProxy_5__setitem__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_5__setitem__;
}
}
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy___next__.doc = __pyx_doc_10TabProxies_10TupleProxy___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___next__;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_8__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_8__next__.doc = __pyx_doc_10TabProxies_10TupleProxy_8__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_8__next__;
}
}
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy___str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy___str__.doc = __pyx_doc_10TabProxies_10TupleProxy___str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___str__;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_9__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy_9__str__.doc = __pyx_doc_10TabProxies_10TupleProxy_9__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_9__str__;
}
}
if (__Pyx_SetVtable(__pyx_type_10TabProxies_TupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_TupleProxy = &__pyx_type_10TabProxies_TupleProxy;
__pyx_vtabptr_10TabProxies_GTFProxy = &__pyx_vtable_10TabProxies_GTFProxy;
__pyx_vtable_10TabProxies_GTFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
- #if PY_MAJOR_VERSION >= 3
__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8GTFProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
- *(void(**)(void))&__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8GTFProxy_update;
- #endif
__pyx_type_10TabProxies_GTFProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__.doc = __pyx_doc_10TabProxies_8GTFProxy___getattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__;
+ __pyx_wrapperbase_10TabProxies_8GTFProxy_8__getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8GTFProxy_8__getattr__.doc = __pyx_doc_10TabProxies_8GTFProxy_8__getattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8GTFProxy_8__getattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_GTFProxy = &__pyx_type_10TabProxies_GTFProxy;
__pyx_vtabptr_10TabProxies_NamedTupleProxy = &__pyx_vtable_10TabProxies_NamedTupleProxy;
__pyx_vtable_10TabProxies_NamedTupleProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
__pyx_type_10TabProxies_NamedTupleProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__.doc = __pyx_doc_10TabProxies_15NamedTupleProxy___setattr__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_NamedTupleProxy = &__pyx_type_10TabProxies_NamedTupleProxy;
__pyx_vtabptr_10TabProxies_BedProxy = &__pyx_vtable_10TabProxies_BedProxy;
__pyx_vtable_10TabProxies_BedProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
- #if PY_MAJOR_VERSION >= 3
__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8BedProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
- *(void(**)(void))&__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8BedProxy_update;
- #endif
__pyx_type_10TabProxies_BedProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_BedProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_BedProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8BedProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8BedProxy___setattr__.doc = __pyx_doc_10TabProxies_8BedProxy___setattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8BedProxy___setattr__;
+ __pyx_wrapperbase_10TabProxies_8BedProxy_1__setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8BedProxy_1__setattr__.doc = __pyx_doc_10TabProxies_8BedProxy_1__setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8BedProxy_1__setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_vtable_10TabProxies_VCFProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8VCFProxy_update;
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+ if (__Pyx_SetAttrString(__pyx_m, "VCFProxy", (PyObject *)&__pyx_type_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":1
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "/ifs/apps/apps/python-2.7.1/lib/python2.7/site-packages/Cython-0.13-py2.7-linux-x86_64.egg/Cython/Includes/cpython/type.pxd":2
+ /* "cpython/type.pxd":2
*
* cdef extern from "Python.h": # <<<<<<<<<<<<<<
* # The C structure of the objects used to describe built-in types.
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
if (__pyx_m) {
__Pyx_AddTraceback("init TabProxies");
Py_DECREF(__pyx_m); __pyx_m = 0;
return result;
}
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
+bad:
+ return;
+}
+#endif
+
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
int exact,
return 0;
}
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "need more than %d value%s to unpack", (int)index,
+ #else
+ "need more than %zd value%s to unpack", index,
+ #endif
+ (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "too many values to unpack (expected %d)", (int)expected);
+ #else
+ "too many values to unpack (expected %zd)", expected);
+ #endif
+}
+
+static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
+ PyObject *item;
+ if (!(item = PyIter_Next(iter))) {
+ if (!PyErr_Occurred()) {
+ __Pyx_RaiseNeedMoreValuesError(index);
+ }
+ }
+ return item;
+}
+
+static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
+ PyObject *item;
+ if ((item = PyIter_Next(iter))) {
+ Py_DECREF(item);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ }
+ else if (!PyErr_Occurred())
+ return 0;
+ else
+ return -1;
+}
+
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name,
PyObject* kw_name)
return (double)-1;
}
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "need more than %d value%s to unpack", (int)index,
- #else
- "need more than %zd value%s to unpack", index,
- #endif
- (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- #if PY_VERSION_HEX < 0x02050000
- "too many values to unpack (expected %d)", (int)expected);
- #else
- "too many values to unpack (expected %zd)", expected);
- #endif
-}
-
-static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
- PyObject *item;
- if (!(item = PyIter_Next(iter))) {
- if (!PyErr_Occurred()) {
- __Pyx_RaiseNeedMoreValuesError(index);
- }
- }
- return item;
-}
-
-static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
- PyObject *item;
- if ((item = PyIter_Next(iter))) {
- Py_DECREF(item);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- }
- else if (!PyErr_Occurred())
- return 0;
- else
- return -1;
-}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
return module;
}
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-}
-
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
-
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-
-#else /* Python 3+ */
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
-
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
-
- PyErr_SetObject(type, value);
-
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-
-bad:
- return;
-}
-#endif
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
const int is_unsigned = const_zero < neg_one;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
-/* Generated by Cython 0.13 on Thu May 5 15:40:49 2011 */
+/* Generated by Cython 0.14.1 on Sat Oct 15 05:27:48 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#define PyBytes_Repr PyString_Repr
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
#endif
-
#ifndef PySet_CheckExact
-# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
#define PyInt_Check(op) PyLong_Check(op)
#define PyInt_CheckExact(op) PyLong_CheckExact(op)
#endif
#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
+ #define PyBoolObject PyLongObject
#endif
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
#endif
+#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
+ #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
+ #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
+#else
+ #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
+ #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
+ #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
+ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
+ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
+ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
+#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
#include "bgzf.h"
#include "tabix.h"
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+
/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
#define CYTHON_INLINE inline
#else
- #define CYTHON_INLINE
+ #define CYTHON_INLINE
#endif
#endif
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
# elif defined(__ICC) || defined(__INTEL_COMPILER)
-# define CYTHON_UNUSED __attribute__ ((__unused__))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
-# define CYTHON_UNUSED
+# define CYTHON_UNUSED
# endif
#endif
#ifdef __GNUC__
/* Test for GCC > 2.95 */
-#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#else /* __GNUC__ > 2 ... */
/* Type declarations */
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
int bedfields;
};
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+/* "cvcf.pyx":94
* ###########################################################################################################
*
* cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "pysam/ctabix.pxd":178
+/* "ctabix.pxd":178
* cdef tabix_t * tabixfile
*
* cdef class Parser: # <<<<<<<<<<<<<<
PyObject_HEAD
};
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221
+/* "cvcf.pyx":221
*
*
* cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
PyObject *vcffile;
};
-/* "pysam/ctabix.pxd":172
+/* "ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
};
-/* "pysam/TabProxies.pxd":42
+/* "TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "pysam/TabProxies.pxd":77
+/* "TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "pysam/TabProxies.pxd":91
+/* "TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
-/* "pysam/TabProxies.pxd":60
+/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+/* "cvcf.pyx":94
* ###########################################################################################################
*
* cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
-/* "pysam/TabProxies.pxd":80
+/* "TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name, PyObject* kw_name); /*proto*/
-
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_name); /*proto*/
+
static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
#define __Pyx_PyObject_AsDouble(obj) \
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
-static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*proto*/
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname); /*proto*/
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+#define __pyx_binding_PyCFunctionType_USED 1
+
+typedef struct {
+ PyCFunctionObject func;
+} __pyx_binding_PyCFunctionType_object;
+
+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
+#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
+
+static int __pyx_binding_PyCFunctionType_init(void); /* proto */
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0;
static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0;
#define __Pyx_MODULE_NAME "cvcf"
-int __pyx_module_is_main_cvcf = 0;
+static int __pyx_module_is_main_cvcf = 0;
/* Implementation of cvcf */
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_NotImplementedError;
static char __pyx_k_1[] = "";
static char __pyx_k_2[] = ",";
-static char __pyx_k_3[] = ":";
-static char __pyx_k_4[] = "-";
-static char __pyx_k_5[] = "Don't understand region string '%s'";
-static char __pyx_k_6[] = ".";
-static char __pyx_k_7[] = ";";
-static char __pyx_k_8[] = "=";
-static char __pyx_k_9[] = "BAD_NUMBER_OF_VALUES";
-static char __pyx_k_10[] = "(found %s values in element %s; expected %s)";
-static char __pyx_k_11[] = "BAD_NUMBER_OF_PARAMETERS";
-static char __pyx_k_12[] = "id=%s, expected %s parameters, got %s";
-static char __pyx_k_14[] = "Line %s: '%s'\n%s %s: %s\n";
-static char __pyx_k_16[] = "<";
-static char __pyx_k_17[] = "V40_MISSING_ANGLE_BRACKETS";
-static char __pyx_k_18[] = ">";
-static char __pyx_k_19[] = "\"";
-static char __pyx_k_20[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
-static char __pyx_k_21[] = "BADLY_FORMATTED_FORMAT_STRING";
-static char __pyx_k_22[] = "ID=";
-static char __pyx_k_23[] = "Number=";
-static char __pyx_k_24[] = "Type=";
-static char __pyx_k_25[] = "Description=";
-static char __pyx_k_26[] = "FORMAT_MISSING_QUOTES";
-static char __pyx_k_27[] = "<none>";
-static char __pyx_k_28[] = "#alleles";
-static char __pyx_k_29[] = "#nonref_alleles";
-static char __pyx_k_30[] = "#genotypes";
-static char __pyx_k_31[] = "#phased_genotypes";
-static char __pyx_k_33[] = "Unknown number type encountered: %s";
-static char __pyx_k_34[] = "%s=%s";
-static char __pyx_k_35[] = "(Undefined tag)";
-static char __pyx_k_38[] = "(output)";
-static char __pyx_k_39[] = "Genotype Quality";
-static char __pyx_k_40[] = "Read depth at this position for this sample";
-static char __pyx_k_41[] = "Haplotype Quality";
-static char __pyx_k_42[] = "Sample Genotype Filter";
-static char __pyx_k_43[] = "##";
-static char __pyx_k_44[] = "VCFv3.3";
-static char __pyx_k_45[] = "VCFv4.0";
-static char __pyx_k_46[] = "VCFv4.1";
-static char __pyx_k_47[] = "UNKNOWN_FORMAT_STRING";
-static char __pyx_k_48[] = "##fileformat=VCFv%s.%s\n";
-static char __pyx_k_49[] = "##%s=%s\n";
-static char __pyx_k_50[] = "#";
-static char __pyx_k_51[] = "\t";
-static char __pyx_k_52[] = "HEADING_NOT_SEPARATED_BY_TABS";
-static char __pyx_k_53[] = "(%sth entry not found)";
-static char __pyx_k_54[] = "(found %s, expected %s)";
-static char __pyx_k_55[] = "BADLY_FORMATTED_HEADING";
-static char __pyx_k_56[] = "\n";
-static char __pyx_k_57[] = "|";
-static char __pyx_k_58[] = "ERROR_FLAG_HAS_VALUE";
-static char __pyx_k_59[] = "ERROR_FORMAT_NOT_NUMERICAL";
-static char __pyx_k_60[] = "ERROR_FORMAT_NOT_CHAR";
-static char __pyx_k_62[] = "BAD_NUMBER_OF_COLUMNS";
-static char __pyx_k_63[] = "expected %s for %s samples (%s), got %s";
-static char __pyx_k_64[] = "(reference is %s, VCF says %s)";
-static char __pyx_k_65[] = "V33_UNMATCHED_DELETION";
-static char __pyx_k_66[] = "(deletion is %s, reference is %s)";
-static char __pyx_k_67[] = "MISSING_INDEL_ALLELE_REF_BASE";
-static char __pyx_k_68[] = "Required key %s not found in data";
-static char __pyx_k_69[] = "enter_default_format";
-static char __pyx_k_70[] = "Can only handle v3.3 and v4.0 VCF files";
-static char __pyx_k_71[] = "Invalid error string: %s";
-static char __pyx_k_72[] = "needs to be checked";
-static char __pyx_k_73[] = "[|/\\\\]";
-static char __pyx_k_74[] = "^[ACGTN]+$";
-static char __pyx_k_75[] = "id numbertype number type description missingvalue";
-static char __pyx_k_76[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
-static char __pyx_k_77[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
-static char __pyx_k_78[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
-static char __pyx_k_79[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
-static char __pyx_k_80[] = "POS_NOT_NUMERICAL:Position column is not numerical";
-static char __pyx_k_81[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
-static char __pyx_k_82[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
-static char __pyx_k_83[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
-static char __pyx_k_84[] = "POS_NOT_POSITIVE:Position field must be >0";
-static char __pyx_k_85[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
-static char __pyx_k_86[] = "ERROR_INFO_STRING:Error while parsing info field";
-static char __pyx_k_87[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
-static char __pyx_k_88[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
-static char __pyx_k_89[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
-static char __pyx_k_90[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
-static char __pyx_k_91[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
-static char __pyx_k_92[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
-static char __pyx_k_93[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
-static char __pyx_k_94[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
-static char __pyx_k_95[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
-static char __pyx_k_96[] = "MISSING_REF:Reference allele missing";
-static char __pyx_k_97[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
-static char __pyx_k_98[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
-static char __pyx_k_99[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k_4[] = ":";
+static char __pyx_k_6[] = "-";
+static char __pyx_k_8[] = "Don't understand region string '%s'";
+static char __pyx_k_9[] = ".";
+static char __pyx_k_11[] = ";";
+static char __pyx_k_14[] = "=";
+static char __pyx_k_18[] = "BAD_NUMBER_OF_VALUES";
+static char __pyx_k_19[] = "(found %s values in element %s; expected %s)";
+static char __pyx_k_20[] = "BAD_NUMBER_OF_PARAMETERS";
+static char __pyx_k_21[] = "id=%s, expected %s parameters, got %s";
+static char __pyx_k_25[] = "Line %s: '%s'\n%s %s: %s\n";
+static char __pyx_k_27[] = "<";
+static char __pyx_k_29[] = "V40_MISSING_ANGLE_BRACKETS";
+static char __pyx_k_30[] = ">";
+static char __pyx_k_34[] = "\"";
+static char __pyx_k_38[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
+static char __pyx_k_39[] = "BADLY_FORMATTED_FORMAT_STRING";
+static char __pyx_k_40[] = "ID=";
+static char __pyx_k_41[] = "Number=";
+static char __pyx_k_42[] = "Type=";
+static char __pyx_k_43[] = "Description=";
+static char __pyx_k_52[] = "FORMAT_MISSING_QUOTES";
+static char __pyx_k_55[] = "<none>";
+static char __pyx_k_56[] = "#alleles";
+static char __pyx_k_57[] = "#nonref_alleles";
+static char __pyx_k_58[] = "#genotypes";
+static char __pyx_k_59[] = "#phased_genotypes";
+static char __pyx_k_61[] = "Unknown number type encountered: %s";
+static char __pyx_k_62[] = "%s=%s";
+static char __pyx_k_63[] = "(Undefined tag)";
+static char __pyx_k_66[] = "(output)";
+static char __pyx_k_69[] = "Genotype Quality";
+static char __pyx_k_70[] = "Read depth at this position for this sample";
+static char __pyx_k_71[] = "Haplotype Quality";
+static char __pyx_k_72[] = "Sample Genotype Filter";
+static char __pyx_k_73[] = "##";
+static char __pyx_k_76[] = "VCFv3.3";
+static char __pyx_k_77[] = "VCFv4.0";
+static char __pyx_k_78[] = "VCFv4.1";
+static char __pyx_k_79[] = "UNKNOWN_FORMAT_STRING";
+static char __pyx_k_80[] = "##fileformat=VCFv%s.%s\n";
+static char __pyx_k_81[] = "##%s=%s\n";
+static char __pyx_k_82[] = "#";
+static char __pyx_k_85[] = "\t";
+static char __pyx_k_87[] = "HEADING_NOT_SEPARATED_BY_TABS";
+static char __pyx_k_88[] = "(%sth entry not found)";
+static char __pyx_k_89[] = "(found %s, expected %s)";
+static char __pyx_k_90[] = "BADLY_FORMATTED_HEADING";
+static char __pyx_k_91[] = "\n";
+static char __pyx_k_92[] = "|";
+static char __pyx_k_93[] = "ERROR_FLAG_HAS_VALUE";
+static char __pyx_k_97[] = "ERROR_FORMAT_NOT_NUMERICAL";
+static char __pyx_k_98[] = "ERROR_FORMAT_NOT_CHAR";
static char __pyx_k__0[] = "0";
static char __pyx_k__D[] = "D";
static char __pyx_k__I[] = "I";
static char __pyx_k__N[] = "N";
-static char __pyx_k_100[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
-static char __pyx_k_101[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
-static char __pyx_k_102[] = "WRONG_REF:Wrong reference %s";
-static char __pyx_k_103[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
-static char __pyx_k_104[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
-static char __pyx_k_105[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
-static char __pyx_k_106[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
-static char __pyx_k_107[] = "VCF.getsamples (line 880)";
-static char __pyx_k_108[] = "VCF.setsamples (line 884)";
-static char __pyx_k_109[] = "VCF.getheader (line 888)";
-static char __pyx_k_110[] = "VCF.setheader (line 892)";
-static char __pyx_k_111[] = "VCF.getinfo (line 896)";
-static char __pyx_k_112[] = "VCF.setinfo (line 900)";
-static char __pyx_k_113[] = "VCF.getformat (line 904)";
-static char __pyx_k_114[] = "VCF.setformat (line 908)";
-static char __pyx_k_115[] = "VCF.getfilter (line 912)";
-static char __pyx_k_116[] = "VCF.setfilter (line 916)";
-static char __pyx_k_117[] = "VCF.setreference (line 927)";
-static char __pyx_k_118[] = "VCF.parse (line 939)";
-static char __pyx_k_119[] = "VCF.write (line 946)";
-static char __pyx_k_120[] = "VCF.writeheader (line 952)";
-static char __pyx_k_121[] = "VCF.compare_calls (line 957)";
-static char __pyx_k_122[] = "VCF.connect (line 979)";
-static char __pyx_k_123[] = "VCF.fetch (line 984)";
-static char __pyx_k_124[] = "VCF.validate (line 993)";
+static char __pyx_k_101[] = "BAD_NUMBER_OF_COLUMNS";
+static char __pyx_k_102[] = "expected %s for %s samples (%s), got %s";
+static char __pyx_k_103[] = "(reference is %s, VCF says %s)";
+static char __pyx_k_111[] = "V33_UNMATCHED_DELETION";
+static char __pyx_k_112[] = "(deletion is %s, reference is %s)";
+static char __pyx_k_113[] = "MISSING_INDEL_ALLELE_REF_BASE";
+static char __pyx_k_115[] = "Required key %s not found in data";
+static char __pyx_k_118[] = "enter_default_format";
+static char __pyx_k_119[] = "Can only handle v3.3 and v4.0 VCF files";
+static char __pyx_k_121[] = "Invalid error string: %s";
+static char __pyx_k_122[] = "needs to be checked";
+static char __pyx_k_126[] = "[|/\\\\]";
+static char __pyx_k_128[] = "^[ACGTN]+$";
+static char __pyx_k_130[] = "id numbertype number type description missingvalue";
+static char __pyx_k_132[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
+static char __pyx_k_133[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
+static char __pyx_k_134[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
+static char __pyx_k_135[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
+static char __pyx_k_136[] = "POS_NOT_NUMERICAL:Position column is not numerical";
+static char __pyx_k_137[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
+static char __pyx_k_138[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
+static char __pyx_k_139[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
+static char __pyx_k_140[] = "POS_NOT_POSITIVE:Position field must be >0";
+static char __pyx_k_141[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
+static char __pyx_k_142[] = "ERROR_INFO_STRING:Error while parsing info field";
+static char __pyx_k_143[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
+static char __pyx_k_144[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
+static char __pyx_k_145[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
+static char __pyx_k_146[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
+static char __pyx_k_147[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
+static char __pyx_k_148[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
+static char __pyx_k_149[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
+static char __pyx_k_150[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
+static char __pyx_k_151[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
+static char __pyx_k_152[] = "MISSING_REF:Reference allele missing";
+static char __pyx_k_153[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
+static char __pyx_k_154[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
+static char __pyx_k_155[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k_156[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
+static char __pyx_k_157[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
+static char __pyx_k_158[] = "WRONG_REF:Wrong reference %s";
+static char __pyx_k_159[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
+static char __pyx_k_160[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
+static char __pyx_k_161[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
+static char __pyx_k_162[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
static char __pyx_k__DP[] = "DP";
static char __pyx_k__FT[] = "FT";
static char __pyx_k__GQ[] = "GQ";
static char __pyx_k__alt1[] = "alt1";
static char __pyx_k__alt2[] = "alt2";
static char __pyx_k__copy[] = "copy";
+static char __pyx_k__cvcf[] = "cvcf";
static char __pyx_k__data[] = "data";
static char __pyx_k__find[] = "find";
static char __pyx_k__info[] = "info";
static char __pyx_k__String[] = "String";
static char __pyx_k___lines[] = "_lines";
static char __pyx_k___parse[] = "_parse";
+static char __pyx_k__append[] = "append";
static char __pyx_k__bisect[] = "bisect";
static char __pyx_k__buffer[] = "buffer";
static char __pyx_k__contig[] = "contig";
static char __pyx_k__datagenerator[] = "datagenerator";
static char __pyx_k__format_format[] = "format_format";
static char __pyx_k__parse_heading[] = "parse_heading";
+static char __pyx_k__parse_regions[] = "parse_regions";
static char __pyx_k__write_heading[] = "write_heading";
static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF";
static PyObject *__pyx_kp_s_1;
-static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_100;
-static PyObject *__pyx_kp_s_101;
+static PyObject *__pyx_n_s_101;
static PyObject *__pyx_kp_s_102;
static PyObject *__pyx_kp_s_103;
-static PyObject *__pyx_kp_s_104;
-static PyObject *__pyx_kp_s_105;
-static PyObject *__pyx_kp_s_106;
-static PyObject *__pyx_kp_u_107;
-static PyObject *__pyx_kp_u_108;
-static PyObject *__pyx_kp_u_109;
-static PyObject *__pyx_n_s_11;
-static PyObject *__pyx_kp_u_110;
-static PyObject *__pyx_kp_u_111;
-static PyObject *__pyx_kp_u_112;
-static PyObject *__pyx_kp_u_113;
-static PyObject *__pyx_kp_u_114;
-static PyObject *__pyx_kp_u_115;
-static PyObject *__pyx_kp_u_116;
-static PyObject *__pyx_kp_u_117;
-static PyObject *__pyx_kp_u_118;
-static PyObject *__pyx_kp_u_119;
-static PyObject *__pyx_kp_s_12;
-static PyObject *__pyx_kp_u_120;
-static PyObject *__pyx_kp_u_121;
-static PyObject *__pyx_kp_u_122;
-static PyObject *__pyx_kp_u_123;
-static PyObject *__pyx_kp_u_124;
+static PyObject *__pyx_kp_s_11;
+static PyObject *__pyx_n_s_111;
+static PyObject *__pyx_kp_s_112;
+static PyObject *__pyx_n_s_113;
+static PyObject *__pyx_kp_s_115;
+static PyObject *__pyx_n_s_118;
+static PyObject *__pyx_kp_s_119;
+static PyObject *__pyx_kp_s_121;
+static PyObject *__pyx_kp_s_122;
+static PyObject *__pyx_kp_s_126;
+static PyObject *__pyx_kp_s_128;
+static PyObject *__pyx_kp_s_130;
+static PyObject *__pyx_kp_s_132;
+static PyObject *__pyx_kp_s_133;
+static PyObject *__pyx_kp_s_134;
+static PyObject *__pyx_kp_s_135;
+static PyObject *__pyx_kp_s_136;
+static PyObject *__pyx_kp_s_137;
+static PyObject *__pyx_kp_s_138;
+static PyObject *__pyx_kp_s_139;
static PyObject *__pyx_kp_s_14;
-static PyObject *__pyx_kp_s_16;
-static PyObject *__pyx_n_s_17;
-static PyObject *__pyx_kp_s_18;
+static PyObject *__pyx_kp_s_140;
+static PyObject *__pyx_kp_s_141;
+static PyObject *__pyx_kp_s_142;
+static PyObject *__pyx_kp_s_143;
+static PyObject *__pyx_kp_s_144;
+static PyObject *__pyx_kp_s_145;
+static PyObject *__pyx_kp_s_146;
+static PyObject *__pyx_kp_s_147;
+static PyObject *__pyx_kp_s_148;
+static PyObject *__pyx_kp_s_149;
+static PyObject *__pyx_kp_s_150;
+static PyObject *__pyx_kp_s_151;
+static PyObject *__pyx_kp_s_152;
+static PyObject *__pyx_kp_s_153;
+static PyObject *__pyx_kp_s_154;
+static PyObject *__pyx_kp_s_155;
+static PyObject *__pyx_kp_s_156;
+static PyObject *__pyx_kp_s_157;
+static PyObject *__pyx_kp_s_158;
+static PyObject *__pyx_kp_s_159;
+static PyObject *__pyx_kp_s_160;
+static PyObject *__pyx_kp_s_161;
+static PyObject *__pyx_kp_s_162;
+static PyObject *__pyx_n_s_18;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_n_s_20;
-static PyObject *__pyx_n_s_21;
-static PyObject *__pyx_kp_s_22;
-static PyObject *__pyx_kp_s_23;
-static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_kp_s_21;
static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_n_s_26;
static PyObject *__pyx_kp_s_27;
-static PyObject *__pyx_kp_s_28;
-static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_3;
+static PyObject *__pyx_n_s_29;
static PyObject *__pyx_kp_s_30;
-static PyObject *__pyx_kp_s_31;
-static PyObject *__pyx_kp_s_33;
static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_35;
-static PyObject *__pyx_kp_s_38;
-static PyObject *__pyx_kp_s_39;
+static PyObject *__pyx_n_s_38;
+static PyObject *__pyx_n_s_39;
static PyObject *__pyx_kp_s_4;
static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_41;
static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
-static PyObject *__pyx_kp_s_44;
-static PyObject *__pyx_kp_s_45;
-static PyObject *__pyx_kp_s_46;
-static PyObject *__pyx_n_s_47;
-static PyObject *__pyx_kp_s_48;
-static PyObject *__pyx_kp_s_49;
-static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_50;
-static PyObject *__pyx_kp_s_51;
static PyObject *__pyx_n_s_52;
-static PyObject *__pyx_kp_s_53;
-static PyObject *__pyx_kp_s_54;
-static PyObject *__pyx_n_s_55;
+static PyObject *__pyx_kp_s_55;
static PyObject *__pyx_kp_s_56;
static PyObject *__pyx_kp_s_57;
-static PyObject *__pyx_n_s_58;
-static PyObject *__pyx_n_s_59;
-static PyObject *__pyx_kp_b_6;
+static PyObject *__pyx_kp_s_58;
+static PyObject *__pyx_kp_s_59;
static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_n_s_60;
-static PyObject *__pyx_n_s_62;
+static PyObject *__pyx_kp_s_61;
+static PyObject *__pyx_kp_s_62;
static PyObject *__pyx_kp_s_63;
-static PyObject *__pyx_kp_s_64;
-static PyObject *__pyx_n_s_65;
static PyObject *__pyx_kp_s_66;
-static PyObject *__pyx_n_s_67;
-static PyObject *__pyx_kp_s_68;
-static PyObject *__pyx_n_s_69;
-static PyObject *__pyx_kp_s_7;
+static PyObject *__pyx_kp_s_69;
static PyObject *__pyx_kp_s_70;
static PyObject *__pyx_kp_s_71;
static PyObject *__pyx_kp_s_72;
static PyObject *__pyx_kp_s_73;
-static PyObject *__pyx_kp_s_74;
-static PyObject *__pyx_kp_s_75;
static PyObject *__pyx_kp_s_76;
static PyObject *__pyx_kp_s_77;
static PyObject *__pyx_kp_s_78;
-static PyObject *__pyx_kp_s_79;
+static PyObject *__pyx_n_s_79;
static PyObject *__pyx_kp_s_8;
static PyObject *__pyx_kp_s_80;
static PyObject *__pyx_kp_s_81;
static PyObject *__pyx_kp_s_82;
-static PyObject *__pyx_kp_s_83;
-static PyObject *__pyx_kp_s_84;
static PyObject *__pyx_kp_s_85;
-static PyObject *__pyx_kp_s_86;
-static PyObject *__pyx_kp_s_87;
+static PyObject *__pyx_n_s_87;
static PyObject *__pyx_kp_s_88;
static PyObject *__pyx_kp_s_89;
-static PyObject *__pyx_n_s_9;
-static PyObject *__pyx_kp_s_90;
+static PyObject *__pyx_kp_b_9;
+static PyObject *__pyx_kp_s_9;
+static PyObject *__pyx_n_s_90;
static PyObject *__pyx_kp_s_91;
static PyObject *__pyx_kp_s_92;
-static PyObject *__pyx_kp_s_93;
-static PyObject *__pyx_kp_s_94;
-static PyObject *__pyx_kp_s_95;
-static PyObject *__pyx_kp_s_96;
-static PyObject *__pyx_kp_s_97;
-static PyObject *__pyx_kp_s_98;
-static PyObject *__pyx_kp_s_99;
+static PyObject *__pyx_n_s_93;
+static PyObject *__pyx_n_s_97;
+static PyObject *__pyx_n_s_98;
+static PyObject *__pyx_kp_b__0;
static PyObject *__pyx_kp_s__0;
static PyObject *__pyx_n_s__ACGTN;
static PyObject *__pyx_n_s__ALT;
static PyObject *__pyx_n_s__NT_UNKNOWN;
static PyObject *__pyx_n_s__NotImplementedError;
static PyObject *__pyx_n_s__Number;
+static PyObject *__pyx_n_b__PASS;
static PyObject *__pyx_n_s__PASS;
static PyObject *__pyx_n_s__POS;
static PyObject *__pyx_n_s__POS_NOT_NUMERICAL;
static PyObject *__pyx_n_s__alt;
static PyObject *__pyx_n_s__alt1;
static PyObject *__pyx_n_s__alt2;
+static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__bisect;
static PyObject *__pyx_n_s__buffer;
static PyObject *__pyx_n_s__chrom;
static PyObject *__pyx_n_s__convertGT;
static PyObject *__pyx_n_s__convertGTback;
static PyObject *__pyx_n_s__copy;
+static PyObject *__pyx_n_s__cvcf;
static PyObject *__pyx_n_s__data;
static PyObject *__pyx_n_s__datagenerator;
static PyObject *__pyx_n_s__deepcopy;
static PyObject *__pyx_n_s__parse_formatdata;
static PyObject *__pyx_n_s__parse_header;
static PyObject *__pyx_n_s__parse_heading;
+static PyObject *__pyx_n_s__parse_regions;
static PyObject *__pyx_n_s__parser;
static PyObject *__pyx_n_s__pos;
static PyObject *__pyx_n_s__pos1;
static PyObject *__pyx_int_40;
static PyObject *__pyx_int_100;
static PyObject *__pyx_int_3000000000;
-static PyObject *__pyx_k_13;
-static PyObject *__pyx_k_15;
-static PyObject *__pyx_k_32;
-static PyObject *__pyx_k_36;
-static PyObject *__pyx_k_37;
-static PyObject *__pyx_k_61;
-
-/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":58
+static PyObject *__pyx_k_22;
+static PyObject *__pyx_k_26;
+static PyObject *__pyx_k_60;
+static PyObject *__pyx_k_64;
+static PyObject *__pyx_k_65;
+static PyObject *__pyx_k_99;
+static PyObject *__pyx_k_tuple_3;
+static PyObject *__pyx_k_tuple_5;
+static PyObject *__pyx_k_tuple_7;
+static PyObject *__pyx_k_tuple_10;
+static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_13;
+static PyObject *__pyx_k_tuple_15;
+static PyObject *__pyx_k_tuple_16;
+static PyObject *__pyx_k_tuple_17;
+static PyObject *__pyx_k_tuple_23;
+static PyObject *__pyx_k_tuple_24;
+static PyObject *__pyx_k_tuple_28;
+static PyObject *__pyx_k_tuple_31;
+static PyObject *__pyx_k_tuple_32;
+static PyObject *__pyx_k_tuple_33;
+static PyObject *__pyx_k_tuple_35;
+static PyObject *__pyx_k_tuple_36;
+static PyObject *__pyx_k_tuple_37;
+static PyObject *__pyx_k_tuple_44;
+static PyObject *__pyx_k_tuple_45;
+static PyObject *__pyx_k_tuple_46;
+static PyObject *__pyx_k_tuple_47;
+static PyObject *__pyx_k_tuple_48;
+static PyObject *__pyx_k_tuple_49;
+static PyObject *__pyx_k_tuple_50;
+static PyObject *__pyx_k_tuple_51;
+static PyObject *__pyx_k_tuple_53;
+static PyObject *__pyx_k_tuple_54;
+static PyObject *__pyx_k_tuple_67;
+static PyObject *__pyx_k_tuple_68;
+static PyObject *__pyx_k_tuple_74;
+static PyObject *__pyx_k_tuple_75;
+static PyObject *__pyx_k_tuple_83;
+static PyObject *__pyx_k_tuple_84;
+static PyObject *__pyx_k_tuple_86;
+static PyObject *__pyx_k_tuple_94;
+static PyObject *__pyx_k_tuple_95;
+static PyObject *__pyx_k_tuple_96;
+static PyObject *__pyx_k_tuple_100;
+static PyObject *__pyx_k_tuple_104;
+static PyObject *__pyx_k_tuple_105;
+static PyObject *__pyx_k_tuple_106;
+static PyObject *__pyx_k_tuple_107;
+static PyObject *__pyx_k_tuple_108;
+static PyObject *__pyx_k_tuple_109;
+static PyObject *__pyx_k_tuple_110;
+static PyObject *__pyx_k_tuple_114;
+static PyObject *__pyx_k_tuple_116;
+static PyObject *__pyx_k_tuple_117;
+static PyObject *__pyx_k_tuple_120;
+static PyObject *__pyx_k_tuple_123;
+static PyObject *__pyx_k_tuple_124;
+static PyObject *__pyx_k_tuple_125;
+static PyObject *__pyx_k_tuple_127;
+static PyObject *__pyx_k_tuple_129;
+static PyObject *__pyx_k_tuple_131;
+
+/* "cvcf.pyx":58
*
* # Utility function. Uses 0-based coordinates
* def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
*/
static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_4cvcf_get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pf_4cvcf_get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)};
static PyObject *__pyx_pf_4cvcf_get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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- {&__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_n_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 1},
{&__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_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_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_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_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_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 0},
{&__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_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_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_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 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_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_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_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_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 0},
{&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0},
{&__pyx_kp_s_71, __pyx_k_71, sizeof(__pyx_k_71), 0, 0, 1, 0},
{&__pyx_kp_s_72, __pyx_k_72, sizeof(__pyx_k_72), 0, 0, 1, 0},
{&__pyx_kp_s_73, __pyx_k_73, sizeof(__pyx_k_73), 0, 0, 1, 0},
- {&__pyx_kp_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 0},
- {&__pyx_kp_s_75, __pyx_k_75, sizeof(__pyx_k_75), 0, 0, 1, 0},
{&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0},
{&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0},
{&__pyx_kp_s_78, __pyx_k_78, sizeof(__pyx_k_78), 0, 0, 1, 0},
- {&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0},
+ {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1},
{&__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_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_n_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 1},
{&__pyx_kp_s_88, __pyx_k_88, sizeof(__pyx_k_88), 0, 0, 1, 0},
{&__pyx_kp_s_89, __pyx_k_89, sizeof(__pyx_k_89), 0, 0, 1, 0},
- {&__pyx_n_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 1},
- {&__pyx_kp_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 0},
+ {&__pyx_kp_b_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 0, 0},
+ {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
+ {&__pyx_n_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 1},
{&__pyx_kp_s_91, __pyx_k_91, sizeof(__pyx_k_91), 0, 0, 1, 0},
{&__pyx_kp_s_92, __pyx_k_92, sizeof(__pyx_k_92), 0, 0, 1, 0},
- {&__pyx_kp_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 0},
- {&__pyx_kp_s_94, __pyx_k_94, sizeof(__pyx_k_94), 0, 0, 1, 0},
- {&__pyx_kp_s_95, __pyx_k_95, sizeof(__pyx_k_95), 0, 0, 1, 0},
- {&__pyx_kp_s_96, __pyx_k_96, sizeof(__pyx_k_96), 0, 0, 1, 0},
- {&__pyx_kp_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 0},
- {&__pyx_kp_s_98, __pyx_k_98, sizeof(__pyx_k_98), 0, 0, 1, 0},
- {&__pyx_kp_s_99, __pyx_k_99, sizeof(__pyx_k_99), 0, 0, 1, 0},
+ {&__pyx_n_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 1},
+ {&__pyx_n_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 1},
+ {&__pyx_n_s_98, __pyx_k_98, sizeof(__pyx_k_98), 0, 0, 1, 1},
+ {&__pyx_kp_b__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 0, 0},
{&__pyx_kp_s__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 1, 0},
{&__pyx_n_s__ACGTN, __pyx_k__ACGTN, sizeof(__pyx_k__ACGTN), 0, 0, 1, 1},
{&__pyx_n_s__ALT, __pyx_k__ALT, sizeof(__pyx_k__ALT), 0, 0, 1, 1},
{&__pyx_n_s__NT_UNKNOWN, __pyx_k__NT_UNKNOWN, sizeof(__pyx_k__NT_UNKNOWN), 0, 0, 1, 1},
{&__pyx_n_s__NotImplementedError, __pyx_k__NotImplementedError, sizeof(__pyx_k__NotImplementedError), 0, 0, 1, 1},
{&__pyx_n_s__Number, __pyx_k__Number, sizeof(__pyx_k__Number), 0, 0, 1, 1},
+ {&__pyx_n_b__PASS, __pyx_k__PASS, sizeof(__pyx_k__PASS), 0, 0, 0, 1},
{&__pyx_n_s__PASS, __pyx_k__PASS, sizeof(__pyx_k__PASS), 0, 0, 1, 1},
{&__pyx_n_s__POS, __pyx_k__POS, sizeof(__pyx_k__POS), 0, 0, 1, 1},
{&__pyx_n_s__POS_NOT_NUMERICAL, __pyx_k__POS_NOT_NUMERICAL, sizeof(__pyx_k__POS_NOT_NUMERICAL), 0, 0, 1, 1},
{&__pyx_n_s__alt, __pyx_k__alt, sizeof(__pyx_k__alt), 0, 0, 1, 1},
{&__pyx_n_s__alt1, __pyx_k__alt1, sizeof(__pyx_k__alt1), 0, 0, 1, 1},
{&__pyx_n_s__alt2, __pyx_k__alt2, sizeof(__pyx_k__alt2), 0, 0, 1, 1},
+ {&__pyx_n_s__append, __pyx_k__append, sizeof(__pyx_k__append), 0, 0, 1, 1},
{&__pyx_n_s__bisect, __pyx_k__bisect, sizeof(__pyx_k__bisect), 0, 0, 1, 1},
{&__pyx_n_s__buffer, __pyx_k__buffer, sizeof(__pyx_k__buffer), 0, 0, 1, 1},
{&__pyx_n_s__chrom, __pyx_k__chrom, sizeof(__pyx_k__chrom), 0, 0, 1, 1},
{&__pyx_n_s__convertGT, __pyx_k__convertGT, sizeof(__pyx_k__convertGT), 0, 0, 1, 1},
{&__pyx_n_s__convertGTback, __pyx_k__convertGTback, sizeof(__pyx_k__convertGTback), 0, 0, 1, 1},
{&__pyx_n_s__copy, __pyx_k__copy, sizeof(__pyx_k__copy), 0, 0, 1, 1},
+ {&__pyx_n_s__cvcf, __pyx_k__cvcf, sizeof(__pyx_k__cvcf), 0, 0, 1, 1},
{&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1},
{&__pyx_n_s__datagenerator, __pyx_k__datagenerator, sizeof(__pyx_k__datagenerator), 0, 0, 1, 1},
{&__pyx_n_s__deepcopy, __pyx_k__deepcopy, sizeof(__pyx_k__deepcopy), 0, 0, 1, 1},
{&__pyx_n_s__parse_formatdata, __pyx_k__parse_formatdata, sizeof(__pyx_k__parse_formatdata), 0, 0, 1, 1},
{&__pyx_n_s__parse_header, __pyx_k__parse_header, sizeof(__pyx_k__parse_header), 0, 0, 1, 1},
{&__pyx_n_s__parse_heading, __pyx_k__parse_heading, sizeof(__pyx_k__parse_heading), 0, 0, 1, 1},
+ {&__pyx_n_s__parse_regions, __pyx_k__parse_regions, sizeof(__pyx_k__parse_regions), 0, 0, 1, 1},
{&__pyx_n_s__parser, __pyx_k__parser, sizeof(__pyx_k__parser), 0, 0, 1, 1},
{&__pyx_n_s__pos, __pyx_k__pos, sizeof(__pyx_k__pos), 0, 0, 1, 1},
{&__pyx_n_s__pos1, __pyx_k__pos1, sizeof(__pyx_k__pos1), 0, 0, 1, 1},
return -1;
}
-static int __Pyx_InitGlobals(void) {
- #if PY_VERSION_HEX < 0x02040000
- if (unlikely(__Pyx_Py23SetsImport() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_2 = PyInt_FromLong(2); if (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 = __LINE__; goto __pyx_L1_error;};
- __pyx_int_26 = PyInt_FromLong(26); if (unlikely(!__pyx_int_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_27 = PyInt_FromLong(27); if (unlikely(!__pyx_int_27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_28 = PyInt_FromLong(28); if (unlikely(!__pyx_int_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_29 = PyInt_FromLong(29); if (unlikely(!__pyx_int_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_30 = PyInt_FromLong(30); if (unlikely(!__pyx_int_30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_33 = PyInt_FromLong(33); if (unlikely(!__pyx_int_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_40 = PyInt_FromLong(40); if (unlikely(!__pyx_int_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_100 = PyInt_FromLong(100); if (unlikely(!__pyx_int_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_int_3000000000 = PyInt_FromString((char *)"3000000000", 0, 0); if (unlikely(!__pyx_int_3000000000)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ * #
+ */
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "pysam/ctabix.pxd":2
+ /* "ctabix.pxd":2
*
* cdef extern from "string.h": # <<<<<<<<<<<<<<
* ctypedef int size_t
__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;
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,
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[],
}
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
- if (unlikely(tstate->curexc_type))
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *local_type, *local_value, *local_tb;
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+ if (unlikely(tstate->curexc_type))
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ #endif
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ /* Make sure tstate is in a consistent state when we XDECREF
+ these objects (XDECREF may run arbitrary code). */
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
goto bad;
- #endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
- return 0;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
+ return;
}
-
+#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
return module;
}
-static PyObject *__Pyx_CreateClass(
- PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
-{
- PyObject *py_modname;
- PyObject *result = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_modname = PyString_FromString(modname);
- #else
- py_modname = PyUnicode_FromString(modname);
- #endif
- if (!py_modname)
- goto bad;
- if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
- goto bad;
- #if PY_MAJOR_VERSION < 3
- result = PyClass_New(bases, dict, name);
- #else
- result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
- #endif
-bad:
- Py_XDECREF(py_modname);
- return result;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
-
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
+static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
+ PyObject *metaclass;
+ /* Default metaclass */
+#if PY_MAJOR_VERSION < 3
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = PyObject_GetAttrString(base, "__class__");
+ if (!metaclass) {
+ PyErr_Clear();
+ metaclass = (PyObject*) Py_TYPE(base);
+ }
+ } else {
+ metaclass = (PyObject *) &PyClass_Type;
+ }
+#else
+ if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
+ PyObject *base = PyTuple_GET_ITEM(bases, 0);
+ metaclass = (PyObject*) Py_TYPE(base);
+ } else {
+ metaclass = (PyObject *) &PyType_Type;
+ }
+#endif
+ Py_INCREF(metaclass);
+ return metaclass;
}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
-
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-}
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
+ PyObject *modname) {
+ PyObject *result;
+ PyObject *metaclass;
+ if (PyDict_SetItemString(dict, "__module__", modname) < 0)
+ return NULL;
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
- Py_INCREF(value);
- }
- #if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
- #else
- if (!PyType_Check(type))
- #endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
+ /* Python2 __metaclass__ */
+ metaclass = PyDict_GetItemString(dict, "__metaclass__");
+ if (metaclass) {
+ Py_INCREF(metaclass);
+ } else {
+ metaclass = __Pyx_FindPy2Metaclass(bases);
}
-
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
+ result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL);
+ Py_DECREF(metaclass);
+ return result;
}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
+ __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
+ if (op == NULL)
+ return NULL;
+ op->func.m_ml = ml;
+ Py_XINCREF(self);
+ op->func.m_self = self;
+ Py_XINCREF(module);
+ op->func.m_module = module;
+ PyObject_GC_Track(op);
+ return (PyObject *)op;
+}
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
+ PyObject_GC_UnTrack(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
+ PyObject_GC_Del(m);
+}
- PyErr_SetObject(type, value);
+static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
+ if (obj == Py_None)
+ obj = NULL;
+ return PyMethod_New(func, obj, type);
+}
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
+static int __pyx_binding_PyCFunctionType_init(void) {
+ __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
+ __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
+ __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
+ __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
+ if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
+ return -1;
}
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
+ return 0;
-bad:
- return;
}
-#endif
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
if (!result)
goto bad;
if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
+ PyErr_Format(PyExc_TypeError,
"%s.%s is not a type object",
module_name, class_name);
goto bad;
}
if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
+ PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
#if PY_VERSION_HEX < 0x02050000
#endif
}
else if (((PyTypeObject *)result)->tp_basicsize != size) {
- PyErr_Format(PyExc_ValueError,
+ PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
goto bad;
}
#endif
-static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+static void* __Pyx_GetVtable(PyObject *dict) {
+ void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
if (!ob)
goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+ ptr = PyCapsule_GetPointer(ob, 0);
#else
- *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+ ptr = PyCObject_AsVoidPtr(ob);
#endif
- if (!*(void **)vtabptr)
- goto bad;
+ if (!ptr && !PyErr_Occurred())
+ PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
Py_DECREF(ob);
- return 0;
+ return ptr;
bad:
Py_XDECREF(ob);
- return -1;
+ return NULL;
}
static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
projects / pysam.git / commitdiff