-/* Generated by Cython 0.14.1 on Fri Nov 25 20:32:50 2011 */
+/* Generated by Cython 0.13 on Thu May 5 14:57:46 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 "tabix.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[] = {
"ctabix.pyx",
"bool.pxd",
- "complex.pxd",
"TabProxies.pxd",
};
/* Type declarations */
-/* "ctabix.pxd":178
+/* "pysam/ctabix.pxd":178
* cdef tabix_t * tabixfile
*
* cdef class Parser: # <<<<<<<<<<<<<<
PyObject_HEAD
};
-/* "ctabix.pyx":389
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":293
* return r
*
* cdef class asVCF( Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a VCF record with
- * the following fields:
+ * '''converts a :term:`tabix row` into a VCF record.'''
+ * def __call__(self, char * buffer, int len ):
*/
struct __pyx_obj_6ctabix_asVCF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":42
+/* "pysam/TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
int is_modified;
};
-/* "TabProxies.pxd":78
+/* "pysam/TabProxies.pxd":77
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
};
-/* "TabProxies.pxd":81
+/* "pysam/TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
int bedfields;
};
-/* "TabProxies.pxd":92
+/* "pysam/TabProxies.pxd":91
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
uint32_t pos;
};
-/* "TabProxies.pxd":61
+/* "pysam/TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
int hasOwnAttributes;
};
-/* "ctabix.pyx":193
- * if self._filename != NULL: free( self._filename )
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":161
+ * return result
*
* cdef class TabixIterator: # <<<<<<<<<<<<<<
* """iterates over rows in *tabixfile* in region
tabix_t *tabixfile;
};
-/* "ctabix.pyx":428
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":304
* #########################################################
* #########################################################
* cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
struct __pyx_obj_6ctabix_Parser *parser;
};
-/* "ctabix.pyx":248
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":216
* ti_iter_destroy(self.iterator)
*
* cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
tabix_t *tabixfile;
};
-/* "ctabix.pxd":172
+/* "pysam/ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
+ * cdef char * filename
*
*/
struct __pyx_obj_6ctabix_Tabixfile {
PyObject_HEAD
- char *_filename;
+ char *filename;
tabix_t *tabixfile;
};
-/* "ctabix.pyx":312
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":277
* return r
*
* cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a GTF record with the following
- * fields:
+ * '''converts a :term:`tabix row` into a GTF record.'''
+ * def __call__(self, char * buffer, int len):
*/
struct __pyx_obj_6ctabix_asGTF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pyx":349
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":285
* return r
*
* cdef class asBed( Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a bed record
- * with the following fields:
+ * '''converts a :term:`tabix row` into a GTF record.'''
+ * def __call__(self, char * buffer, int len):
*/
struct __pyx_obj_6ctabix_asBed {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pyx":299
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":267
* pass
*
* cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a python tuple.
- *
+ * '''converts a :term:`tabix row` into a python tuple.'''
+ * def __call__(self, char * buffer, int len):
*/
struct __pyx_obj_6ctabix_asTuple {
};
-/* "TabProxies.pxd":42
+/* "pysam/TabProxies.pxd":42
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "TabProxies.pxd":78
+/* "pysam/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;
-/* "TabProxies.pxd":92
+/* "pysam/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;
-/* "TabProxies.pxd":81
+/* "pysam/TabProxies.pxd":80
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
-/* "TabProxies.pxd":61
+/* "pysam/TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name, PyObject* kw_name); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
-
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
return r;
}
-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 void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
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 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 int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
static void __Pyx_AddTraceback(const char *funcname); /*proto*/
/* 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 PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0;
static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0;
#define __Pyx_MODULE_NAME "ctabix"
-static int __pyx_module_is_main_ctabix = 0;
+int __pyx_module_is_main_ctabix = 0;
/* Implementation of ctabix */
static PyObject *__pyx_builtin_IOError;
static char __pyx_k_9[] = "start out of range (%i)";
static char __pyx_k_10[] = "end out of range (%i)";
static char __pyx_k_11[] = "I/O operation on closed file";
-static char __pyx_k_14[] = "malformatted query or wrong sequence name.\n";
-static char __pyx_k_16[] = "can't open header.\n";
-static char __pyx_k_20[] = "Filename '%s' already exists, use *force* to overwrite";
-static char __pyx_k_21[] = "could not open '%s' for writing";
-static char __pyx_k_23[] = "could not open '%s' for reading";
-static char __pyx_k_25[] = "writing failed";
-static char __pyx_k_29[] = "#";
-static char __pyx_k_31[] = "No such file '%s'";
-static char __pyx_k_32[] = ".gz";
-static char __pyx_k_34[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
-static char __pyx_k_42[] = "unknown preset '%s', valid presets are '%s'";
-static char __pyx_k_43[] = ",";
-static char __pyx_k_44[] = "filename associated with this object.";
-static char __pyx_k_45[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
-static char __pyx_k_46[] = "chromosome names";
+static char __pyx_k_12[] = "malformatted query or wrong sequence name.\n";
+static char __pyx_k_13[] = "can't open header.\n";
+static char __pyx_k_15[] = "Filename '%s' already exists, use *force* to overwrite";
+static char __pyx_k_16[] = "could not open '%s' for writing";
+static char __pyx_k_17[] = "could not open '%s' for reading";
+static char __pyx_k_18[] = "writing failed";
+static char __pyx_k_20[] = "#";
+static char __pyx_k_22[] = "No such file '%s'";
+static char __pyx_k_23[] = ".gz";
+static char __pyx_k_24[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
+static char __pyx_k_25[] = "unknown preset '%s', valid presets are '%s'";
+static char __pyx_k_26[] = ",";
+static char __pyx_k_27[] = "chromosome names";
+static char __pyx_k_28[] = "Tabixfile._isOpen (line 19)";
+static char __pyx_k_29[] = "Tabixfile._open (line 23)";
+static char __pyx_k_30[] = "Tabixfile._parseRegion (line 57)";
+static char __pyx_k_31[] = "Tabixfile.fetch (line 102)";
+static char __pyx_k_32[] = "Tabixfile.header.__get__ (line 140)";
+static char __pyx_k_33[] = "TabixIterator.__next__ (line 192)";
+static char __pyx_k_34[] = "TabixHeaderIterator.__next__ (line 239)";
+static char __pyx_k_35[] = "TabixIteratorParsed.__next__ (line 342)";
+static char __pyx_k_36[] = "tabix_compress (line 362)";
+static char __pyx_k_37[] = "tabix_index (line 407)";
static char __pyx_k__r[] = "r";
static char __pyx_k__w[] = "w";
static char __pyx_k__bc[] = "bc";
static char __pyx_k__asGTF[] = "asGTF";
static char __pyx_k__asVCF[] = "asVCF";
static char __pyx_k__close[] = "close";
+static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__force[] = "force";
static char __pyx_k__start[] = "start";
static char __pyx_k__types[] = "types";
-static char __pyx_k__append[] = "append";
static char __pyx_k__buffer[] = "buffer";
-static char __pyx_k__ctabix[] = "ctabix";
static char __pyx_k__ctypes[] = "ctypes";
static char __pyx_k__exists[] = "exists";
+static char __pyx_k__header[] = "header";
static char __pyx_k__parser[] = "parser";
static char __pyx_k__pileup[] = "pileup";
static char __pyx_k__preset[] = "preset";
static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__OSError[] = "OSError";
static char __pyx_k____all__[] = "__all__";
+static char __pyx_k____get__[] = "__get__";
static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k__asTuple[] = "asTuple";
static char __pyx_k__end_col[] = "end_col";
static char __pyx_k__KeyError[] = "KeyError";
static char __pyx_k__O_RDONLY[] = "O_RDONLY";
static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____next__[] = "__next__";
static char __pyx_k____test__[] = "__test__";
static char __pyx_k__endswith[] = "endswith";
static char __pyx_k__filename[] = "filename";
static char __pyx_k__iterator[] = "iterator";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__Tabixfile[] = "Tabixfile";
-static char __pyx_k___filename[] = "_filename";
static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__line_skip[] = "line_skip";
static char __pyx_k__meta_char[] = "meta_char";
static char __pyx_k___parseRegion[] = "_parseRegion";
static char __pyx_k__filename_out[] = "filename_out";
static char __pyx_k__StopIteration[] = "StopIteration";
+static char __pyx_k__TabixIterator[] = "TabixIterator";
static char __pyx_k__tabix_compress[] = "tabix_compress";
+static char __pyx_k__TabixHeaderIterator[] = "TabixHeaderIterator";
+static char __pyx_k__TabixIteratorParsed[] = "TabixIteratorParsed";
static PyObject *__pyx_kp_s_1;
static PyObject *__pyx_kp_s_10;
static PyObject *__pyx_kp_s_11;
-static PyObject *__pyx_kp_s_14;
+static PyObject *__pyx_kp_s_12;
+static PyObject *__pyx_kp_s_13;
+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_s_20;
-static PyObject *__pyx_kp_s_21;
+static PyObject *__pyx_kp_s_22;
static PyObject *__pyx_kp_s_23;
+static PyObject *__pyx_kp_s_24;
static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_kp_s_29;
+static PyObject *__pyx_kp_s_26;
+static PyObject *__pyx_kp_u_28;
+static PyObject *__pyx_kp_u_29;
static PyObject *__pyx_kp_s_3;
-static PyObject *__pyx_kp_s_31;
-static PyObject *__pyx_kp_s_32;
-static PyObject *__pyx_kp_s_34;
+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_s_4;
-static PyObject *__pyx_kp_s_42;
-static PyObject *__pyx_kp_s_43;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_n_s__OSError;
static PyObject *__pyx_n_s__O_RDONLY;
static PyObject *__pyx_n_s__StopIteration;
+static PyObject *__pyx_n_s__TabixHeaderIterator;
+static PyObject *__pyx_n_s__TabixIterator;
+static PyObject *__pyx_n_s__TabixIteratorParsed;
static PyObject *__pyx_n_s__Tabixfile;
static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____all__;
+static PyObject *__pyx_n_s____get__;
static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____next__;
static PyObject *__pyx_n_s____test__;
-static PyObject *__pyx_n_s___filename;
static PyObject *__pyx_n_s___isOpen;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
-static PyObject *__pyx_n_s__append;
static PyObject *__pyx_n_s__asBed;
static PyObject *__pyx_n_s__asGTF;
static PyObject *__pyx_n_s__asTuple;
static PyObject *__pyx_n_s__buffer;
static PyObject *__pyx_n_s__close;
static PyObject *__pyx_n_s__copy;
-static PyObject *__pyx_n_s__ctabix;
static PyObject *__pyx_n_s__ctypes;
static PyObject *__pyx_n_s__ec;
static PyObject *__pyx_n_s__end;
static PyObject *__pyx_n_s__end_col;
static PyObject *__pyx_n_s__endswith;
static PyObject *__pyx_n_s__exists;
+static PyObject *__pyx_n_s__fetch;
static PyObject *__pyx_n_s__filename;
static PyObject *__pyx_n_s__filename_in;
static PyObject *__pyx_n_s__filename_out;
static PyObject *__pyx_n_s__fp;
static PyObject *__pyx_n_s__gff;
static PyObject *__pyx_n_s__gzip;
+static PyObject *__pyx_n_s__header;
static PyObject *__pyx_n_s__idx;
static PyObject *__pyx_n_s__iterator;
static PyObject *__pyx_n_s__itertools;
static PyObject *__pyx_int_15;
static PyObject *__pyx_int_17;
static PyObject *__pyx_int_18;
-static PyObject *__pyx_int_65536;
+static PyObject *__pyx_int_0x10000;
+static PyObject *__pyx_k_14;
static PyObject *__pyx_k_19;
-static PyObject *__pyx_k_28;
-static PyObject *__pyx_k_30;
-static PyObject *__pyx_k_tuple_12;
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values[2] = ((PyObject *)Py_None);
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- /* "ctabix.pyx":619
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- {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_46), 0},
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.Tabixfile"), /*tp_name*/
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0, /*tp_clear*/
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__Pyx_NAMESTR("ctabix.Parser"), /*tp_name*/
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PyErr_Restore(etype, eval, etb);
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- __pyx_pf_6ctabix_13TabixIterator_2__next__, /*tp_iternext*/
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+ __pyx_pf_6ctabix_13TabixIterator___next__, /*tp_iternext*/
__pyx_methods_6ctabix_TabixIterator, /*tp_methods*/
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PyErr_Fetch(&etype, &eval, &etb);
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PyErr_Restore(etype, eval, etb);
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{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.TabixHeaderIterator"), /*tp_name*/
sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
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- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
__Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/
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- __pyx_pf_6ctabix_19TabixHeaderIterator_1__iter__, /*tp_iter*/
- __pyx_pf_6ctabix_19TabixHeaderIterator_2__next__, /*tp_iternext*/
+ __pyx_pf_6ctabix_19TabixHeaderIterator___iter__, /*tp_iter*/
+ __pyx_pf_6ctabix_19TabixHeaderIterator___next__, /*tp_iternext*/
__pyx_methods_6ctabix_TabixHeaderIterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asTuple = {
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/
sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/
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- __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
#endif
};
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/
sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/
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+ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asBed = {
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.asBed"), /*tp_name*/
sizeof(struct __pyx_obj_6ctabix_asBed), /*tp_basicsize*/
0, /*tp_getattro*/
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+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asVCF = {
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.asVCF"), /*tp_name*/
sizeof(struct __pyx_obj_6ctabix_asVCF), /*tp_basicsize*/
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+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_6ctabix_19TabixIteratorParsed_3__dealloc__(o);
+ __pyx_pf_6ctabix_19TabixIteratorParsed___dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
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+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_6ctabix_19TabixIteratorParsed___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixIteratorParsed___next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
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PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("ctabix.TabixIteratorParsed"), /*tp_name*/
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__Pyx_DOCSTR("iterates over mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/
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__pyx_tp_clear_6ctabix_TabixIteratorParsed, /*tp_clear*/
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0, /*tp_weaklistoffset*/
- __pyx_pf_6ctabix_19TabixIteratorParsed_1__iter__, /*tp_iter*/
- __pyx_pf_6ctabix_19TabixIteratorParsed_2__next__, /*tp_iternext*/
+ __pyx_pf_6ctabix_19TabixIteratorParsed___iter__, /*tp_iter*/
+ __pyx_pf_6ctabix_19TabixIteratorParsed___next__, /*tp_iternext*/
__pyx_methods_6ctabix_TabixIteratorParsed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
};
static PyMethodDef __pyx_methods[] = {
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#if PY_MAJOR_VERSION < 3
PyMODINIT_FUNC initctabix(void); /*proto*/
#endif
{
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if (PyType_Ready(&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_Tabixfile = &__pyx_type_6ctabix_Tabixfile;
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if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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}
- if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{
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if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
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- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed_2__next__;
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+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed___next__;
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+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__TabixIterator); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____next__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_33), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__TabixHeaderIterator); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____next__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_34), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__TabixIteratorParsed); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____next__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_35), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_compress); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_36), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_index); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_37), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "cpython/type.pxd":2
+ /* "/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
*
* cdef extern from "Python.h": # <<<<<<<<<<<<<<
* # The C structure of the objects used to describe built-in types.
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
if (__pyx_m) {
__Pyx_AddTraceback("init ctabix");
Py_DECREF(__pyx_m); __pyx_m = 0;
#endif
}
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *number, *more_or_less;
+
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ number = (num_expected == 1) ? "" : "s";
+ PyErr_Format(PyExc_TypeError,
+ #if PY_VERSION_HEX < 0x02050000
+ "%s() takes %s %d positional argument%s (%d given)",
+ #else
+ "%s() takes %s %zd positional argument%s (%zd given)",
+ #endif
+ func_name, more_or_less, num_expected, number, num_found);
+}
+
static int __Pyx_ParseOptionalKeywords(
PyObject *kwds,
PyObject **argnames[],
return -1;
}
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *number, *more_or_less;
-
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- number = (num_expected == 1) ? "" : "s";
- PyErr_Format(PyExc_TypeError,
- #if PY_VERSION_HEX < 0x02050000
- "%s() takes %s %d positional argument%s (%d given)",
- #else
- "%s() takes %s %zd positional argument%s (%zd given)",
- #endif
- func_name, more_or_less, num_expected, number, num_found);
-}
-
-
-static 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 void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
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 int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
const int32_t neg_one = (int32_t)-1, const_zero = (int32_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;
}
#endif
-static void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
if (!ob)
goto bad;
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- ptr = PyCapsule_GetPointer(ob, 0);
+ *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
#else
- ptr = PyCObject_AsVoidPtr(ob);
+ *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
+ if (!*(void **)vtabptr)
+ goto bad;
Py_DECREF(ob);
- return ptr;
+ return 0;
bad:
Py_XDECREF(ob);
- return NULL;
+ return -1;
}
#include "compile.h"
projects / pysam.git / blobdiff