-/* Generated by Cython 0.17.2 on Wed Jan 23 09:18:14 2013 */
+/* Generated by Cython 0.15.1 on Mon Jan 14 23:52:53 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
#else
+
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
+
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
#define __fastcall
#endif
#endif
+
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
+
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+ #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+ #define PyDict_Contains(d,o) PySequence_Contains(d,o)
#endif
+
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
+ #define PyNumber_Index(o) PyNumber_Int(o)
+ #define PyIndex_Check(o) PyNumber_Check(o)
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
+
typedef struct {
void *buf;
PyObject *obj;
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
+
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
+
#endif
+
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
+
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
+
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
#define PyBytes_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)
#ifndef PySet_CheckExact
#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_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
+
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
+
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
#if (PY_MAJOR_VERSION < 3) || (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)
(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
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) (n)
#endif
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
#ifndef __PYX_EXTERN_C
#ifdef __cplusplus
#define __PYX_EXTERN_C extern "C"
#define _USE_MATH_DEFINES
#endif
#include <math.h>
-#define __PYX_HAVE__pysam__csamtools
-#define __PYX_HAVE_API__pysam__csamtools
+#define __PYX_HAVE__csamtools
+#define __PYX_HAVE_API__csamtools
#include "string.h"
#include "stdlib.h"
#include "math.h"
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# elif defined(__ICC) || defined(__INTEL_COMPILER)
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
static const char *__pyx_f[] = {
"csamtools.pyx",
- "type.pxd",
"bool.pxd",
"complex.pxd",
};
+static PyObject *__Pyx_Generator_Next(PyObject *self);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
+static PyObject *__Pyx_Generator_Close(PyObject *self);
+static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds);
+
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
-struct __pyx_obj_5pysam_9csamtools_Samfile;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_5pysam_9csamtools_Fastafile;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumn;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
-struct __pyx_obj_5pysam_9csamtools_IndexedReads;
-struct __pyx_obj_5pysam_9csamtools_SNPCall;
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
-struct __pyx_obj_5pysam_9csamtools_AlignedRead;
-struct __pyx_obj_5pysam_9csamtools_PileupProxy;
-struct __pyx_obj_5pysam_9csamtools_PileupRead;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs;
-struct __pyx_t_5pysam_9csamtools___iterdata;
-typedef struct __pyx_t_5pysam_9csamtools___iterdata __pyx_t_5pysam_9csamtools___iterdata;
-struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData;
-struct __pyx_t_5pysam_9csamtools_MateData;
-typedef struct __pyx_t_5pysam_9csamtools_MateData __pyx_t_5pysam_9csamtools_MateData;
-
-/* "pysam/csamtools.pxd":394
+struct __pyx_Generator_object;
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr;
+struct __pyx_obj_9csamtools_IteratorRow;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs;
+struct __pyx_obj_9csamtools_IteratorRowAll;
+struct __pyx_obj_9csamtools_PileupProxy;
+struct __pyx_obj_9csamtools_AlignedRead;
+struct __pyx_obj_9csamtools_Fastafile;
+struct __pyx_obj_9csamtools_IteratorRowSelection;
+struct __pyx_obj_9csamtools_IteratorColumn;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs;
+struct __pyx_obj_9csamtools_IteratorRowRegion;
+struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_9csamtools_Samfile;
+struct __pyx_obj_9csamtools_SNPCall;
+struct __pyx_obj_9csamtools_IndexedReads;
+struct __pyx_obj_9csamtools_IteratorColumnRegion;
+struct __pyx_obj_9csamtools_PileupRead;
+struct __pyx_t_9csamtools___iterdata;
+typedef struct __pyx_t_9csamtools___iterdata __pyx_t_9csamtools___iterdata;
+struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData;
+struct __pyx_t_9csamtools_MateData;
+typedef struct __pyx_t_9csamtools_MateData __pyx_t_9csamtools_MateData;
+
+/* "csamtools.pxd":394
* # Utility types
*
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
* samfile_t * samfile
* bam_iter_t iter
*/
-struct __pyx_t_5pysam_9csamtools___iterdata {
+struct __pyx_t_9csamtools___iterdata {
samfile_t *samfile;
bam_iter_t iter;
faidx_t *fastafile;
int seq_len;
};
-/* "pysam/csamtools.pxd":523
+/* "csamtools.pxd":523
* cdef char * getSequence( self )
* cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
* int tid,
* int start,
*/
-struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData {
+struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData {
int __pyx_n;
int reopen;
};
-/* "pysam/csamtools.pyx":518
+/* "csamtools.pyx":518
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
* char * name
* bam1_t * mate
*/
-struct __pyx_t_5pysam_9csamtools_MateData {
+struct __pyx_t_9csamtools_MateData {
char *name;
bam1_t *mate;
uint32_t flag;
};
-/* "pysam/csamtools.pxd":464
+/* "csamtools.pyx":140
+ * cdef char* CODE2CIGAR= "MIDNSHP=X"
+ * if IS_PYTHON3:
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
+ */
+struct __pyx_Generator_object {
+ PyObject_HEAD
+ __pyx_generator_body_t body;
+ int is_running;
+ int resume_label;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+};
+
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
+ struct __pyx_Generator_object __pyx_base;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "csamtools.pxd":464
* cdef uint32_t _is_tail
*
* cdef class IteratorRow: # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow {
+struct __pyx_obj_9csamtools_IteratorRow {
PyObject_HEAD
};
-/* "pysam/csamtools.pxd":487
+/* "csamtools.pxd":487
* cdef int cnext(self)
*
* cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
* cdef Samfile samfile
* cdef int tid
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
int tid;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *rowiter;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
};
-/* "pysam/csamtools.pxd":420
- * cdef bam1_t * _delegate
+/* "csamtools.pxd":480
+ * cdef int cnext(self)
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_Samfile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isstream;
- int isremote;
+struct __pyx_obj_9csamtools_IteratorRowAll {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
bam1_t *b;
- char *mode;
- int64_t start_offset;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":492
- * cdef IteratorRowRegion rowiter
+/* "csamtools.pxd":449
+ * cdef char * _getrname( self, int tid )
*
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef int current_pos
+ * cdef class PileupProxy: # <<<<<<<<<<<<<<
+ * cdef bam_pileup1_t ** plp
+ * cdef int tid
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtab;
- bam1_t *b;
- int current_pos;
- samfile_t *fp;
- PyObject *positions;
- int owns_samfile;
+struct __pyx_obj_9csamtools_PileupProxy {
+ PyObject_HEAD
+ bam_pileup1_t **plp;
+ int tid;
+ int pos;
+ int n_pu;
};
-/* "pysam/csamtools.pyx":142
- * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
- * else:
- * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+/* "csamtools.pxd":415
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length )
+ *
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
*
+ * # object that this AlignedRead represents
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
+struct __pyx_obj_9csamtools_AlignedRead {
PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ bam1_t *_delegate;
};
-/* "pysam/csamtools.pxd":408
+/* "csamtools.pxd":408
* # Note: need to declare all C fields and methods here
* #
* cdef class Fastafile: # <<<<<<<<<<<<<<
* cdef char * _filename
* # pointer to fastafile
*/
-struct __pyx_obj_5pysam_9csamtools_Fastafile {
+struct __pyx_obj_9csamtools_Fastafile {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtab;
+ struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
char *_filename;
faidx_t *fastafile;
};
-/* "pysam/csamtools.pxd":467
- * pass
+/* "csamtools.pxd":492
+ * cdef IteratorRowRegion rowiter
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam_iter_t iter # iterator state object
- * cdef bam1_t * b
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef int current_pos
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
+struct __pyx_obj_9csamtools_IteratorRowSelection {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab;
bam1_t *b;
- int retval;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ int current_pos;
samfile_t *fp;
+ PyObject *positions;
int owns_samfile;
};
-/* "pysam/csamtools.pxd":504
+/* "csamtools.pxd":504
* cdef int cnext(self)
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
*
* # result of the last plbuf_push
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorColumn {
+struct __pyx_obj_9csamtools_IteratorColumn {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtab;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *iter;
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *iter;
int tid;
int pos;
int n_plp;
int mask;
const bam_pileup1_t * plp;
bam_plp_t pileup_iter;
- __pyx_t_5pysam_9csamtools___iterdata iterdata;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- struct __pyx_obj_5pysam_9csamtools_Fastafile *fastafile;
+ __pyx_t_9csamtools___iterdata iterdata;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ struct __pyx_obj_9csamtools_Fastafile *fastafile;
PyObject *stepper;
int max_depth;
};
-/* "pysam/csamtools.pxd":531
- * cdef reset( self, tid, start, end )
+/* "csamtools.pxd":536
+ * cdef int truncate
+ *
+ * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * cdef int start
- * cdef int end
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
- int start;
- int end;
- int truncate;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "pysam/csamtools.pxd":480
- * cdef int cnext(self)
+/* "csamtools.pxd":467
+ * pass
*
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef samfile_t * fp
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam_iter_t iter # iterator state object
+ * cdef bam1_t * b
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAll {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtab;
+struct __pyx_obj_9csamtools_IteratorRowRegion {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
+ bam_iter_t iter;
bam1_t *b;
+ int retval;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
samfile_t *fp;
int owns_samfile;
};
-/* "pysam/csamtools.pxd":539
- * pass
+/* "csamtools.pyx":142
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
*
- * cdef class IndexedReads: # <<<<<<<<<<<<<<
- * cdef Samfile samfile
- * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_IndexedReads {
+struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr {
+ struct __pyx_Generator_object __pyx_base;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "csamtools.pxd":420
+ * cdef bam1_t * _delegate
+ *
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
+ */
+struct __pyx_obj_9csamtools_Samfile {
PyObject_HEAD
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- samfile_t *fp;
- PyObject *index;
- int owns_samfile;
+ struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
+ char *_filename;
+ samfile_t *samfile;
+ bam_index_t *index;
+ int isbam;
+ int isstream;
+ int isremote;
+ bam1_t *b;
+ char *mode;
+ int64_t start_offset;
};
-/* "pysam/csamtools.pyx":3222
+/* "csamtools.pyx":3222
* return retval, out_stderr, out_stdout
*
* cdef class SNPCall: # <<<<<<<<<<<<<<
* '''the results of a SNP call.'''
* cdef int _tid
*/
-struct __pyx_obj_5pysam_9csamtools_SNPCall {
+struct __pyx_obj_9csamtools_SNPCall {
PyObject_HEAD
int _tid;
int _pos;
};
-/* "pysam/csamtools.pyx":140
- * cdef char* CODE2CIGAR= "MIDNSHP=X"
- * if IS_PYTHON3:
- * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * else:
- * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
- */
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
- PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
-};
-
-
-/* "pysam/csamtools.pxd":415
- * cdef char * _fetch( self, char * reference, int start, int end, int * length )
- *
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+/* "csamtools.pxd":539
+ * pass
*
- * # object that this AlignedRead represents
+ * cdef class IndexedReads: # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_AlignedRead {
+struct __pyx_obj_9csamtools_IndexedReads {
PyObject_HEAD
- bam1_t *_delegate;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ PyObject *index;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":449
- * cdef char * _getrname( self, int tid )
+/* "csamtools.pxd":531
+ * cdef reset( self, tid, start, end )
*
- * cdef class PileupProxy: # <<<<<<<<<<<<<<
- * cdef bam_pileup1_t ** plp
- * cdef int tid
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * cdef int start
+ * cdef int end
*/
-struct __pyx_obj_5pysam_9csamtools_PileupProxy {
- PyObject_HEAD
- bam_pileup1_t **plp;
- int tid;
- int pos;
- int n_pu;
+struct __pyx_obj_9csamtools_IteratorColumnRegion {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+ int start;
+ int end;
+ int truncate;
};
-/* "pysam/csamtools.pxd":455
+/* "csamtools.pxd":455
* cdef int n_pu
*
* cdef class PileupRead: # <<<<<<<<<<<<<<
* cdef AlignedRead _alignment
* cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_PileupRead {
+struct __pyx_obj_9csamtools_PileupRead {
PyObject_HEAD
- struct __pyx_obj_5pysam_9csamtools_AlignedRead *_alignment;
+ struct __pyx_obj_9csamtools_AlignedRead *_alignment;
int32_t _qpos;
int _indel;
int _level;
};
-/* "pysam/csamtools.pxd":536
- * cdef int truncate
- *
- * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
-};
-
-
-/* "pysam/csamtools.pyx":1766
+/* "csamtools.pyx":1766
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn {
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *);
- char *(*getSequence)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *);
- PyObject *(*setMask)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *);
- PyObject *(*setupIteratorData)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
- PyObject *(*reset)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
+struct __pyx_vtabstruct_9csamtools_IteratorColumn {
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorColumn *);
+ char *(*getSequence)(struct __pyx_obj_9csamtools_IteratorColumn *);
+ PyObject *(*setMask)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *);
+ PyObject *(*setupIteratorData)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
+ PyObject *(*reset)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
-/* "pysam/csamtools.pyx":1540
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
+/* "csamtools.pyx":1931
+ * self.iterdata.seq = NULL
*
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * '''iterates over a region only.
+ * '''
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
+struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion {
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
-/* "pysam/csamtools.pyx":375
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
+/* "csamtools.pyx":1461
+ *
+ *
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
- char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
+struct __pyx_vtabstruct_9csamtools_IteratorRowRegion {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowRegion *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowRegion *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;
-/* "pysam/csamtools.pyx":1461
- *
+/* "csamtools.pyx":1641
+ * raise StopIteration
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
+struct __pyx_vtabstruct_9csamtools_IteratorRowSelection {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
-/* "pysam/csamtools.pyx":1968
+/* "csamtools.pyx":1968
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
* """
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs {
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
-/* "pysam/csamtools.pyx":1641
- * raise StopIteration
+/* "csamtools.pyx":545
*
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile)*
*
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
+ * add_sq_text = False, check_header = True, check_sq = True )*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
+struct __pyx_vtabstruct_9csamtools_Samfile {
+ bam_header_t *(*_buildHeader)(struct __pyx_obj_9csamtools_Samfile *, PyObject *);
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_Samfile *);
+ int (*cnext)(struct __pyx_obj_9csamtools_Samfile *);
+ int (*write)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
+ char *(*_getrname)(struct __pyx_obj_9csamtools_Samfile *, int);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;
-/* "pysam/csamtools.pyx":1931
- * self.iterdata.seq = NULL
+/* "csamtools.pyx":375
+ * ## Public methods
+ * ######################################################################
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion {
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_9csamtools_Fastafile {
+ char *(*_fetch)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;
-/* "pysam/csamtools.pyx":545
+/* "csamtools.pyx":1540
+ * if self.owns_samfile: samclose( self.fp )
*
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int reopen = True)*
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
- * add_sq_text = False, check_header = True, check_sq = True )*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_Samfile {
- bam_header_t *(*_buildHeader)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *);
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_Samfile *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_Samfile *);
- int (*write)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
- char *(*_getrname)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int);
+struct __pyx_vtabstruct_9csamtools_IteratorRowAll {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowAll *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
+
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
+
#if CYTHON_REFNANNY
typedef struct {
void (*INCREF)(void*, PyObject*, int);
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
-#ifdef WITH_THREAD
- #define __Pyx_RefNannySetupContext(name, acquire_gil) \
- if (acquire_gil) { \
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
- PyGILState_Release(__pyx_gilstate_save); \
- } else { \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
- }
-#else
- #define __Pyx_RefNannySetupContext(name, acquire_gil) \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
-#endif
- #define __Pyx_RefNannyFinishContext() \
- __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+ #define __Pyx_RefNannySetupContext(name) __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+ #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
#define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
#define __Pyx_RefNannyDeclarations
- #define __Pyx_RefNannySetupContext(name, acquire_gil)
+ #define __Pyx_RefNannySetupContext(name)
#define __Pyx_RefNannyFinishContext()
#define __Pyx_INCREF(r) Py_INCREF(r)
#define __Pyx_DECREF(r) Py_DECREF(r)
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
#endif /* CYTHON_REFNANNY */
-#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
-#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#ifndef CYTHON_PROFILE
#define CYTHON_PROFILE 1
#endif
+
#ifndef CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_PROFILE_REUSE_FRAME 0
#endif
+
#if CYTHON_PROFILE
+
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
+
#if CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_FRAME_MODIFIER static
#define CYTHON_FRAME_DEL
#define CYTHON_FRAME_MODIFIER
#define CYTHON_FRAME_DEL Py_DECREF(__pyx_frame)
#endif
+
#define __Pyx_TraceDeclarations \
static PyCodeObject *__pyx_frame_code = NULL; \
CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
int __Pyx_use_tracing = 0;
+
#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \
__Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \
}
+
#define __Pyx_TraceException() \
if (unlikely(__Pyx_use_tracing( && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyObject *exc_info = __Pyx_GetExceptionTuple(); \
Py_DECREF(exc_info); \
} \
}
+
#define __Pyx_TraceReturn(result) \
if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyThreadState_GET()->c_profilefunc( \
PyThreadState_GET()->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
CYTHON_FRAME_DEL; \
}
+
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/
+
#else
+
#define __Pyx_TraceDeclarations
#define __Pyx_TraceCall(funcname, srcfile, firstlineno)
#define __Pyx_TraceException()
#define __Pyx_TraceReturn(result)
-#endif /* CYTHON_PROFILE */
-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+#endif /* CYTHON_PROFILE */
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 CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
+ const char* function_name, int kw_allowed); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*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_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_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
Py_DECREF(j);
return r;
}
+
+
#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
+
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
- __Pyx_GetItemInt_Fast(o, i) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i)))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (PyList_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, n);
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
Py_INCREF(r);
return r;
}
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
Py_INCREF(r);
return r;
}
- } else { /* inlined PySequence_GetItem() */
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return NULL;
- i += l;
- }
- return m->sq_item(o, i);
- }
}
-#else
- if (PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len)) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
+
+#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+ PyObject *r;
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
}
- return PyList_Append(list, x);
+ else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
+ r = PySequence_GetItem(o, i);
+ }
+ else {
+ r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ }
+ return r;
}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (unlikely(PyList_Append(L, x) < 0)) return NULL;
+ if (PyList_Append(L, x) < 0) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- } else {
+ }
+ else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
}
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
- int result = PySequence_Contains(seq, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
}
-
-static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
- int result = PyDict_Contains(dict, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
+ return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
}
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
+ if (unlikely(d == Py_None)) {
+ __Pyx_RaiseNoneIndexingError();
+ return NULL;
+ }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
Py_INCREF(value);
#else
if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) {
+ /* these presumably have safe hash functions */
value = PyDict_GetItem(d, key);
if (unlikely(!value)) {
value = default_value;
m = __Pyx_GetAttrString(d, "get");
if (!m) return NULL;
value = PyObject_CallFunctionObjArgs(m, key,
- (default_value == Py_None) ? NULL : default_value, NULL);
+ (default_value == Py_None) ? NULL : default_value, NULL);
Py_DECREF(m);
}
#endif
#define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_DelItemInt_Fast(o, i) : \
__Pyx_DelItem_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
int r;
if (!j) return -1;
Py_DECREF(j);
return r;
}
+
static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_PYPY
- if (PySequence_Check(o)) {
+ if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && likely(i >= 0))
return PySequence_DelItem(o, i);
+ else {
+ PyObject *j = PyInt_FromSsize_t(i);
+ return __Pyx_DelItem_Generic(o, j);
}
-#else
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return -1;
- i += l;
- }
- return m->sq_ass_item(o, i, (PyObject *)NULL);
- }
-#endif
- return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
}
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
-
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_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
PyObject *modname); /*proto*/
-#define __Pyx_CyFunction_USED 1
-#include <structmember.h>
-#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
-#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
-#define __Pyx_CYFUNCTION_CCLASS 0x04
-#define __Pyx_CyFunction_GetClosure(f) \
- (((__pyx_CyFunctionObject *) (f))->func_closure)
-#define __Pyx_CyFunction_GetClassObj(f) \
- (((__pyx_CyFunctionObject *) (f))->func_classobj)
-#define __Pyx_CyFunction_Defaults(type, f) \
- ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
-#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
- ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
+#define __pyx_binding_PyCFunctionType_USED 1
+
typedef struct {
PyCFunctionObject func;
- int flags;
- PyObject *func_dict;
- PyObject *func_weakreflist;
- PyObject *func_name;
- PyObject *func_doc;
- PyObject *func_code;
- PyObject *func_closure;
- PyObject *func_classobj; /* No-args super() class cell */
- void *defaults;
- int defaults_pyobjects;
- PyObject *defaults_tuple; /* Const defaults tuple */
- PyObject *(*defaults_getter)(PyObject *);
-} __pyx_CyFunctionObject;
-static PyTypeObject *__pyx_CyFunctionType = 0;
-#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \
- __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code)
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *,
- PyMethodDef *ml, int flags,
- PyObject *self, PyObject *module,
- PyObject* code);
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
- size_t size,
- int pyobjects);
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
- PyObject *tuple);
-static int __Pyx_CyFunction_init(void);
+} __pyx_binding_PyCFunctionType_object;
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
+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 int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
+
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t);
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
+
static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject *);
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-#define __Pyx_Generator_USED
-#include <structmember.h>
-#include <frameobject.h>
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-typedef struct {
- PyObject_HEAD
- __pyx_generator_body_t body;
- PyObject *closure;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
- PyObject *gi_weakreflist;
- PyObject *classobj;
- PyObject *yieldfrom;
- int resume_label;
- char is_running; // using T_BOOL for property below requires char value
-} __pyx_GeneratorObject;
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure);
-static int __pyx_Generator_init(void);
-static int __Pyx_Generator_clear(PyObject* self);
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
-#else
-#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
-#endif
-
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-#if !defined(__Pyx_PyIdentifier_FromString)
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
-#else
- #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
-#endif
-#endif
-
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
+static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
+ int __pyx_lineno, const char *__pyx_filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-
/* Module declarations from 'cpython.version' */
/* Module declarations from 'cpython.ref' */
/* Module declarations from 'cpython.iterator' */
-/* Module declarations from '__builtin__' */
-
/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
/* Module declarations from 'cpython' */
-/* Module declarations from 'pysam.csamtools' */
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_AlignedRead = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Samfile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupProxy = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupRead = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRow = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowRegion = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAll = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowSelection = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumn = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IndexedReads = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_SNPCall = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = 0;
-static PyObject *__pyx_v_5pysam_9csamtools__FILENAME_ENCODING = 0;
-static char *__pyx_v_5pysam_9csamtools_CODE2CIGAR;
-static char *__pyx_v_5pysam_9csamtools_bam_nt16_rev_table;
-static int __pyx_v_5pysam_9csamtools_max_pos;
-static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *, size_t); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__my_encodeFilename(PyObject *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__force_str(PyObject *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_count_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools___advance_all(void *, bam1_t *); /*proto*/
-static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-#define __Pyx_MODULE_NAME "pysam.csamtools"
-int __pyx_module_is_main_pysam__csamtools = 0;
-
-/* Implementation of 'pysam.csamtools' */
+/* Module declarations from 'csamtools' */
+static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_Generator = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0;
+static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0;
+static char *__pyx_v_9csamtools_CODE2CIGAR;
+static char *__pyx_v_9csamtools_bam_nt16_rev_table;
+static int __pyx_v_9csamtools_max_pos;
+static PyObject *__pyx_f_9csamtools_from_string_and_size(char *, size_t); /*proto*/
+static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools__charptr_to_str(char *); /*proto*/
+static PyObject *__pyx_f_9csamtools__force_str(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
+static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
+static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
+static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
+static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_count_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools___advance_all(void *, bam1_t *); /*proto*/
+static int __pyx_f_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *); /*proto*/
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
+#define __Pyx_MODULE_NAME "csamtools"
+int __pyx_module_is_main_csamtools = 0;
+
+/* Implementation of 'csamtools' */
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_UnicodeDecodeError;
-static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static int __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8gettid(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_14reset(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_16seek(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_18tell(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_28close(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_32write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_42__next__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_other); /* proto */
-static Py_hash_t __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall___str__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_2build(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_4find(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static void __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */
static char __pyx_k_1[] = "Argument must be string or unicode.";
static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
static char __pyx_k_5[] = "\t";
static char __pyx_k__I[] = "I";
static char __pyx_k__S[] = "S";
static char __pyx_k__Z[] = "Z";
-static char __pyx_k__a[] = "a";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
static char __pyx_k_250[] = "MIDNSHP=X";
static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)";
static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_256[] = "/ifs/devel/pysam/pysam/csamtools.pyx";
-static char __pyx_k_257[] = "pysam.csamtools";
-static char __pyx_k_258[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
-static char __pyx_k_267[] = "\n stderr is captured.\n ";
-static char __pyx_k_274[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_291[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+static char __pyx_k_254[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
+static char __pyx_k_255[] = "\n stderr is captured.\n ";
+static char __pyx_k_256[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_262[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
static char __pyx_k__chr[] = "chr";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
-static char __pyx_k__inf[] = "inf";
static char __pyx_k__map[] = "map";
static char __pyx_k__max[] = "max";
static char __pyx_k__min[] = "min";
-static char __pyx_k__ofd[] = "ofd";
static char __pyx_k__ord[] = "ord";
static char __pyx_k__pos[] = "pos";
static char __pyx_k__raw[] = "raw";
static char __pyx_k___open[] = "_open";
static char __pyx_k__ascii[] = "ascii";
static char __pyx_k__bqual[] = "bqual";
-static char __pyx_k__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__flush[] = "flush";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__reopen[] = "reopen";
-static char __pyx_k__retval[] = "retval";
static char __pyx_k__sorted[] = "sorted";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__platform[] = "platform";
static char __pyx_k__samtools[] = "samtools";
-static char __pyx_k__stderr_f[] = "stderr_f";
-static char __pyx_k__stderr_h[] = "stderr_h";
-static char __pyx_k__stdout_f[] = "stdout_f";
-static char __pyx_k__stdout_h[] = "stdout_h";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__template[] = "template";
static char __pyx_k__truncate[] = "truncate";
static char __pyx_k____enter__[] = "__enter__";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__alignment[] = "alignment";
+static char __pyx_k__csamtools[] = "csamtools";
static char __pyx_k__enumerate[] = "enumerate";
static char __pyx_k__exc_value[] = "exc_value";
static char __pyx_k__fastafile[] = "fastafile";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___buildLine[] = "_buildLine";
-static char __pyx_k__out_stderr[] = "out_stderr";
-static char __pyx_k__out_stdout[] = "out_stdout";
static char __pyx_k__references[] = "references";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__AlignedRead[] = "AlignedRead";
static char __pyx_k__defaultdict[] = "defaultdict";
static char __pyx_k__nreferences[] = "nreferences";
static char __pyx_k__snp_quality[] = "snp_quality";
-static char __pyx_k__stdout_save[] = "stdout_save";
static char __pyx_k__IndexedReads[] = "IndexedReads";
static char __pyx_k__PileupColumn[] = "PileupColumn";
static char __pyx_k___parseRegion[] = "_parseRegion";
static PyObject *__pyx_kp_s_24;
static PyObject *__pyx_n_s_249;
static PyObject *__pyx_kp_s_251;
+static PyObject *__pyx_kp_s_254;
+static PyObject *__pyx_kp_s_255;
static PyObject *__pyx_kp_s_256;
-static PyObject *__pyx_n_s_257;
-static PyObject *__pyx_kp_s_258;
-static PyObject *__pyx_kp_s_267;
-static PyObject *__pyx_kp_s_274;
+static PyObject *__pyx_kp_s_262;
static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_291;
static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
static PyObject *__pyx_n_s___samtools_dispatch;
-static PyObject *__pyx_n_s__a;
static PyObject *__pyx_n_s__add_sq_text;
static PyObject *__pyx_n_s__alignment;
static PyObject *__pyx_n_s__all;
static PyObject *__pyx_n_s__c;
static PyObject *__pyx_n_s__calcsize;
static PyObject *__pyx_n_s__callback;
-static PyObject *__pyx_n_s__cargs;
static PyObject *__pyx_n_s__catch_stdout;
static PyObject *__pyx_n_s__check_header;
static PyObject *__pyx_n_s__check_sq;
static PyObject *__pyx_n_s__compile;
static PyObject *__pyx_n_s__consensus_quality;
static PyObject *__pyx_n_s__coverage;
+static PyObject *__pyx_n_s__csamtools;
static PyObject *__pyx_n_s__ctypes;
static PyObject *__pyx_n_s__d;
static PyObject *__pyx_n_s__data_len;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__indel;
static PyObject *__pyx_n_s__index;
-static PyObject *__pyx_n_s__inf;
static PyObject *__pyx_n_s__is_del;
static PyObject *__pyx_n_s__is_head;
static PyObject *__pyx_n_s__is_tail;
static PyObject *__pyx_n_s__nextiter;
static PyObject *__pyx_n_s__nreferences;
static PyObject *__pyx_n_s__object;
-static PyObject *__pyx_n_s__ofd;
static PyObject *__pyx_n_s__offset;
static PyObject *__pyx_n_s__open;
static PyObject *__pyx_n_s__ord;
static PyObject *__pyx_n_s__os;
-static PyObject *__pyx_n_s__out_stderr;
-static PyObject *__pyx_n_s__out_stdout;
static PyObject *__pyx_n_s__pack_into;
static PyObject *__pyx_n_s__path;
static PyObject *__pyx_n_s__pileups;
static PyObject *__pyx_n_s__remove;
static PyObject *__pyx_n_s__reopen;
static PyObject *__pyx_n_s__restore;
-static PyObject *__pyx_n_s__retval;
static PyObject *__pyx_n_s__rlen;
static PyObject *__pyx_n_s__rname;
static PyObject *__pyx_n_s__s;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__stderr;
-static PyObject *__pyx_n_s__stderr_f;
-static PyObject *__pyx_n_s__stderr_h;
static PyObject *__pyx_n_s__stdout;
-static PyObject *__pyx_n_s__stdout_f;
-static PyObject *__pyx_n_s__stdout_h;
-static PyObject *__pyx_n_s__stdout_save;
static PyObject *__pyx_n_s__stepper;
static PyObject *__pyx_n_s__streams;
static PyObject *__pyx_n_s__strip;
static PyObject *__pyx_k_tuple_183;
static PyObject *__pyx_k_tuple_184;
static PyObject *__pyx_k_tuple_252;
-static PyObject *__pyx_k_tuple_254;
+static PyObject *__pyx_k_tuple_257;
+static PyObject *__pyx_k_tuple_258;
static PyObject *__pyx_k_tuple_259;
+static PyObject *__pyx_k_tuple_260;
static PyObject *__pyx_k_tuple_261;
-static PyObject *__pyx_k_tuple_263;
-static PyObject *__pyx_k_tuple_265;
-static PyObject *__pyx_k_tuple_268;
-static PyObject *__pyx_k_tuple_270;
-static PyObject *__pyx_k_tuple_272;
-static PyObject *__pyx_k_tuple_275;
-static PyObject *__pyx_k_tuple_276;
-static PyObject *__pyx_k_tuple_277;
-static PyObject *__pyx_k_tuple_278;
-static PyObject *__pyx_k_tuple_279;
-static PyObject *__pyx_k_tuple_280;
-static PyObject *__pyx_k_tuple_282;
-static PyObject *__pyx_k_tuple_283;
-static PyObject *__pyx_k_tuple_285;
-static PyObject *__pyx_k_tuple_287;
-static PyObject *__pyx_k_tuple_289;
-static PyObject *__pyx_k_tuple_292;
-static PyObject *__pyx_k_codeobj_255;
-static PyObject *__pyx_k_codeobj_260;
-static PyObject *__pyx_k_codeobj_262;
-static PyObject *__pyx_k_codeobj_264;
-static PyObject *__pyx_k_codeobj_266;
-static PyObject *__pyx_k_codeobj_269;
-static PyObject *__pyx_k_codeobj_271;
-static PyObject *__pyx_k_codeobj_273;
-static PyObject *__pyx_k_codeobj_281;
-static PyObject *__pyx_k_codeobj_284;
-static PyObject *__pyx_k_codeobj_286;
-static PyObject *__pyx_k_codeobj_288;
-static PyObject *__pyx_k_codeobj_290;
-static PyObject *__pyx_k_codeobj_293;
-static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-
-/* "pysam/csamtools.pyx":140
+static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
+
+/* "csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
+static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_1genexpr[] = "genexpr()";
+static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("genexpr", 0);
- __pyx_cur_scope = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
+ __Pyx_RefNannySetupContext("genexpr");
+ __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 140);
- {
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_cur_scope);
- __Pyx_RefNannyFinishContext();
- return (PyObject *) gen;
- }
+ __pyx_self = __pyx_self;
+ __pyx_cur_scope->__pyx_base.resume_label = 0;
+ __pyx_cur_scope->__pyx_base.body = (__pyx_generator_body_t) __pyx_gb_9csamtools_2generator;
+ __Pyx_GIVEREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) __pyx_cur_scope;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
{
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *(*__pyx_t_4)(PyObject *);
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("None", 0);
- switch (__pyx_generator->resume_label) {
+ __Pyx_RefNannySetupContext("None");
+ switch (__pyx_cur_scope->__pyx_base.resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_generator->resume_label = 1;
+ __pyx_cur_scope->__pyx_base.resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_generator->resume_label = -1;
- __Pyx_Generator_clear((PyObject*)__pyx_generator);
+ __pyx_cur_scope->__pyx_base.resume_label = -1;
__Pyx_RefNannyFinishContext();
return NULL;
}
-static PyObject *__pyx_gb_5pysam_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
-/* "pysam/csamtools.pyx":142
+/* "csamtools.pyx":142
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
+static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_3genexpr[] = "genexpr()";
+static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("genexpr", 0);
- __pyx_cur_scope = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
+ __Pyx_RefNannySetupContext("genexpr");
+ __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 142);
- {
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_7generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_cur_scope);
- __Pyx_RefNannyFinishContext();
- return (PyObject *) gen;
- }
+ __pyx_self = __pyx_self;
+ __pyx_cur_scope->__pyx_base.resume_label = 0;
+ __pyx_cur_scope->__pyx_base.body = (__pyx_generator_body_t) __pyx_gb_9csamtools_4generator1;
+ __Pyx_GIVEREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) __pyx_cur_scope;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
return __pyx_r;
}
-static PyObject *__pyx_gb_5pysam_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
{
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *(*__pyx_t_4)(PyObject *);
PyObject *__pyx_t_5 = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("None", 0);
- switch (__pyx_generator->resume_label) {
+ __Pyx_RefNannySetupContext("None");
+ switch (__pyx_cur_scope->__pyx_base.resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_x);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_generator->resume_label = 1;
+ __pyx_cur_scope->__pyx_base.resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_generator->resume_label = -1;
- __Pyx_Generator_clear((PyObject*)__pyx_generator);
+ __pyx_cur_scope->__pyx_base.resume_label = -1;
__Pyx_RefNannyFinishContext();
return NULL;
}
-/* "pysam/csamtools.pyx":24
+/* "csamtools.pyx":24
* ########################################################################
* IS_PYTHON3 = PY_MAJOR_VERSION >= 3
* cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<<
* return s[:length]
*/
-static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
+static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("from_string_and_size", 0);
+ __Pyx_RefNannySetupContext("from_string_and_size");
__Pyx_TraceCall("from_string_and_size", __pyx_f[0], 24);
- /* "pysam/csamtools.pyx":25
+ /* "csamtools.pyx":25
* IS_PYTHON3 = PY_MAJOR_VERSION >= 3
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":26
+ /* "csamtools.pyx":26
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3:
* return s[:length] # <<<<<<<<<<<<<<
* return s[:length].decode("ascii")
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromStringAndSize(((const char*)__pyx_v_s) + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
}
/*else*/ {
- /* "pysam/csamtools.pyx":28
+ /* "csamtools.pyx":28
* return s[:length]
* else:
* return s[:length].decode("ascii") # <<<<<<<<<<<<<<
* # filename encoding (copied from lxml.etree.pyx)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":41
+/* "csamtools.pyx":41
* #_C_FILENAME_ENCODING = <char*>_FILENAME_ENCODING
*
* cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<<
* """
*/
-static PyObject *__pyx_f_5pysam_9csamtools__my_encodeFilename(PyObject *__pyx_v_filename) {
+static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_my_encodeFilename", 0);
+ __Pyx_RefNannySetupContext("_my_encodeFilename");
__Pyx_TraceCall("_my_encodeFilename", __pyx_f[0], 41);
- /* "pysam/csamtools.pyx":44
+ /* "csamtools.pyx":44
* u"""Make sure a filename is 8-bit encoded (or None).
* """
* if filename is None: # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_filename == Py_None);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":45
+ /* "csamtools.pyx":45
* """
* if filename is None:
* return None # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":46
+ /* "csamtools.pyx":46
* if filename is None:
* return None
* elif PyBytes_Check(filename): # <<<<<<<<<<<<<<
__pyx_t_1 = PyBytes_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":47
+ /* "csamtools.pyx":47
* return None
* elif PyBytes_Check(filename):
* return filename # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":48
+ /* "csamtools.pyx":48
* elif PyBytes_Check(filename):
* return filename
* elif PyUnicode_Check(filename): # <<<<<<<<<<<<<<
__pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":49
+ /* "csamtools.pyx":49
* return filename
* elif PyUnicode_Check(filename):
* return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<<
__pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_INCREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
__pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
/*else*/ {
- /* "pysam/csamtools.pyx":51
+ /* "csamtools.pyx":51
* return filename.encode(_FILENAME_ENCODING)
* else:
* raise TypeError, u"Argument must be string or unicode." # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":54
+/* "csamtools.pyx":54
*
*
* cdef bytes _force_bytes(object s): # <<<<<<<<<<<<<<
* """
*/
-static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *__pyx_v_s) {
+static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_bytes", 0);
+ __Pyx_RefNannySetupContext("_force_bytes");
__Pyx_TraceCall("_force_bytes", __pyx_f[0], 54);
- /* "pysam/csamtools.pyx":57
+ /* "csamtools.pyx":57
* u"""convert string or unicode object to bytes, assuming ascii encoding.
* """
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":58
+ /* "csamtools.pyx":58
* """
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":59
+ /* "csamtools.pyx":59
* if PY_MAJOR_VERSION < 3:
* return s
* elif s is None: # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_s == Py_None);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":60
+ /* "csamtools.pyx":60
* return s
* elif s is None:
* return None # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":61
+ /* "csamtools.pyx":61
* elif s is None:
* return None
* elif PyBytes_Check(s): # <<<<<<<<<<<<<<
__pyx_t_1 = PyBytes_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":62
+ /* "csamtools.pyx":62
* return None
* elif PyBytes_Check(s):
* return s # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":63
+ /* "csamtools.pyx":63
* elif PyBytes_Check(s):
* return s
* elif PyUnicode_Check(s): # <<<<<<<<<<<<<<
__pyx_t_1 = PyUnicode_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":64
+ /* "csamtools.pyx":64
* return s
* elif PyUnicode_Check(s):
* return s.encode('ascii') # <<<<<<<<<<<<<<
}
/*else*/ {
- /* "pysam/csamtools.pyx":66
+ /* "csamtools.pyx":66
* return s.encode('ascii')
* else:
* raise TypeError, u"Argument must be string, bytes or unicode." # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":68
+/* "csamtools.pyx":68
* raise TypeError, u"Argument must be string, bytes or unicode."
*
* cdef inline bytes _force_cmdline_bytes(object s): # <<<<<<<<<<<<<<
*
*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *__pyx_v_s) {
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_cmdline_bytes", 0);
+ __Pyx_RefNannySetupContext("_force_cmdline_bytes");
__Pyx_TraceCall("_force_cmdline_bytes", __pyx_f[0], 68);
- /* "pysam/csamtools.pyx":69
+ /* "csamtools.pyx":69
*
* cdef inline bytes _force_cmdline_bytes(object s):
* return _force_bytes(s) # <<<<<<<<<<<<<<
* cdef _charptr_to_str(char* s):
*/
__Pyx_XDECREF(((PyObject *)__pyx_r));
- __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":71
+/* "csamtools.pyx":71
* return _force_bytes(s)
*
* cdef _charptr_to_str(char* s): # <<<<<<<<<<<<<<
* return s
*/
-static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *__pyx_v_s) {
+static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_charptr_to_str", 0);
+ __Pyx_RefNannySetupContext("_charptr_to_str");
__Pyx_TraceCall("_charptr_to_str", __pyx_f[0], 71);
- /* "pysam/csamtools.pyx":72
+ /* "csamtools.pyx":72
*
* cdef _charptr_to_str(char* s):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":73
+ /* "csamtools.pyx":73
* cdef _charptr_to_str(char* s):
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
}
/*else*/ {
- /* "pysam/csamtools.pyx":75
+ /* "csamtools.pyx":75
* return s
* else:
* return s.decode("ascii") # <<<<<<<<<<<<<<
* cdef _force_str(object s):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, strlen(__pyx_v_s), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":77
+/* "csamtools.pyx":77
* return s.decode("ascii")
*
* cdef _force_str(object s): # <<<<<<<<<<<<<<
* if s is None:
*/
-static PyObject *__pyx_f_5pysam_9csamtools__force_str(PyObject *__pyx_v_s) {
+static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_str", 0);
+ __Pyx_RefNannySetupContext("_force_str");
__Pyx_TraceCall("_force_str", __pyx_f[0], 77);
- /* "pysam/csamtools.pyx":79
+ /* "csamtools.pyx":79
* cdef _force_str(object s):
* """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
* if s is None: # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_s == Py_None);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":80
+ /* "csamtools.pyx":80
* """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
* if s is None:
* return None # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":81
+ /* "csamtools.pyx":81
* if s is None:
* return None
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":82
+ /* "csamtools.pyx":82
* return None
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
goto __pyx_L4;
}
- /* "pysam/csamtools.pyx":83
+ /* "csamtools.pyx":83
* if PY_MAJOR_VERSION < 3:
* return s
* elif PyBytes_Check(s): # <<<<<<<<<<<<<<
__pyx_t_1 = PyBytes_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":84
+ /* "csamtools.pyx":84
* return s
* elif PyBytes_Check(s):
* return s.decode('ascii') # <<<<<<<<<<<<<<
}
/*else*/ {
- /* "pysam/csamtools.pyx":87
+ /* "csamtools.pyx":87
* else:
* # assume unicode
* return s # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":160
+/* "csamtools.pyx":160
* #####################################################################
* cdef class AlignedRead
* cdef makeAlignedRead(bam1_t * src): # <<<<<<<<<<<<<<
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
-static PyObject *__pyx_f_5pysam_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
- struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_dest = 0;
+static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
+ struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makeAlignedRead", 0);
+ __Pyx_RefNannySetupContext("makeAlignedRead");
__Pyx_TraceCall("makeAlignedRead", __pyx_f[0], 160);
- /* "pysam/csamtools.pyx":162
+ /* "csamtools.pyx":162
* cdef makeAlignedRead(bam1_t * src):
* '''enter src into AlignedRead.'''
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
* dest._delegate = bam_dup1(src)
* return dest
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":163
+ /* "csamtools.pyx":163
* '''enter src into AlignedRead.'''
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = bam_dup1(src) # <<<<<<<<<<<<<<
*/
__pyx_v_dest->_delegate = bam_dup1(__pyx_v_src);
- /* "pysam/csamtools.pyx":164
+ /* "csamtools.pyx":164
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = bam_dup1(src)
* return dest # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.makeAlignedRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.makeAlignedRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":167
+/* "csamtools.pyx":167
*
* cdef class PileupProxy
* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ): # <<<<<<<<<<<<<<
* dest.plp = plp
*/
-static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
- struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_dest = 0;
+static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
+ struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupProxy", 0);
+ __Pyx_RefNannySetupContext("makePileupProxy");
__Pyx_TraceCall("makePileupProxy", __pyx_f[0], 167);
- /* "pysam/csamtools.pyx":168
+ /* "csamtools.pyx":168
* cdef class PileupProxy
* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
* cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) # <<<<<<<<<<<<<<
* dest.plp = plp
* dest.tid = tid
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_PileupProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_PileupProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":169
+ /* "csamtools.pyx":169
* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
* cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
* dest.plp = plp # <<<<<<<<<<<<<<
*/
__pyx_v_dest->plp = __pyx_v_plp;
- /* "pysam/csamtools.pyx":170
+ /* "csamtools.pyx":170
* cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
* dest.plp = plp
* dest.tid = tid # <<<<<<<<<<<<<<
*/
__pyx_v_dest->tid = __pyx_v_tid;
- /* "pysam/csamtools.pyx":171
+ /* "csamtools.pyx":171
* dest.plp = plp
* dest.tid = tid
* dest.pos = pos # <<<<<<<<<<<<<<
*/
__pyx_v_dest->pos = __pyx_v_pos;
- /* "pysam/csamtools.pyx":172
+ /* "csamtools.pyx":172
* dest.tid = tid
* dest.pos = pos
* dest.n = n # <<<<<<<<<<<<<<
if (PyObject_SetAttr(((PyObject *)__pyx_v_dest), __pyx_n_s__n, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":173
+ /* "csamtools.pyx":173
* dest.pos = pos
* dest.n = n
* return dest # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.makePileupProxy", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.makePileupProxy", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":176
+/* "csamtools.pyx":176
*
* cdef class PileupRead
* cdef makePileupRead( bam_pileup1_t * src ): # <<<<<<<<<<<<<<
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
*/
-static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_dest = 0;
+static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
+ struct __pyx_obj_9csamtools_PileupRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- int32_t __pyx_t_2;
- int __pyx_t_3;
- uint32_t __pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupRead", 0);
+ __Pyx_RefNannySetupContext("makePileupRead");
__Pyx_TraceCall("makePileupRead", __pyx_f[0], 176);
- /* "pysam/csamtools.pyx":178
+ /* "csamtools.pyx":178
* cdef makePileupRead( bam_pileup1_t * src ):
* '''fill a PileupRead object from a bam_pileup1_t * object.'''
* cdef PileupRead dest = PileupRead.__new__(PileupRead) # <<<<<<<<<<<<<<
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_PileupRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_PileupRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupRead *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":179
+ /* "csamtools.pyx":179
* '''fill a PileupRead object from a bam_pileup1_t * object.'''
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
* dest._alignment = makeAlignedRead( src.b ) # <<<<<<<<<<<<<<
* dest._qpos = src.qpos
* dest._indel = src.indel
*/
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_src->b); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_src->b); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_AlignedRead))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_v_dest->_alignment);
__Pyx_DECREF(((PyObject *)__pyx_v_dest->_alignment));
- __pyx_v_dest->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_t_1);
+ __pyx_v_dest->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":180
+ /* "csamtools.pyx":180
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos # <<<<<<<<<<<<<<
* dest._indel = src.indel
* dest._level = src.level
*/
- __pyx_t_2 = __pyx_v_src->qpos;
- __pyx_v_dest->_qpos = __pyx_t_2;
+ __pyx_v_dest->_qpos = __pyx_v_src->qpos;
- /* "pysam/csamtools.pyx":181
+ /* "csamtools.pyx":181
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos
* dest._indel = src.indel # <<<<<<<<<<<<<<
* dest._level = src.level
* dest._is_del = src.is_del
*/
- __pyx_t_3 = __pyx_v_src->indel;
- __pyx_v_dest->_indel = __pyx_t_3;
+ __pyx_v_dest->_indel = __pyx_v_src->indel;
- /* "pysam/csamtools.pyx":182
+ /* "csamtools.pyx":182
* dest._qpos = src.qpos
* dest._indel = src.indel
* dest._level = src.level # <<<<<<<<<<<<<<
* dest._is_del = src.is_del
* dest._is_head = src.is_head
*/
- __pyx_t_3 = __pyx_v_src->level;
- __pyx_v_dest->_level = __pyx_t_3;
+ __pyx_v_dest->_level = __pyx_v_src->level;
- /* "pysam/csamtools.pyx":183
+ /* "csamtools.pyx":183
* dest._indel = src.indel
* dest._level = src.level
* dest._is_del = src.is_del # <<<<<<<<<<<<<<
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail
*/
- __pyx_t_4 = __pyx_v_src->is_del;
- __pyx_v_dest->_is_del = __pyx_t_4;
+ __pyx_v_dest->_is_del = __pyx_v_src->is_del;
- /* "pysam/csamtools.pyx":184
+ /* "csamtools.pyx":184
* dest._level = src.level
* dest._is_del = src.is_del
* dest._is_head = src.is_head # <<<<<<<<<<<<<<
* dest._is_tail = src.is_tail
* return dest
*/
- __pyx_t_4 = __pyx_v_src->is_head;
- __pyx_v_dest->_is_head = __pyx_t_4;
+ __pyx_v_dest->_is_head = __pyx_v_src->is_head;
- /* "pysam/csamtools.pyx":185
+ /* "csamtools.pyx":185
* dest._is_del = src.is_del
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail # <<<<<<<<<<<<<<
* return dest
*
*/
- __pyx_t_4 = __pyx_v_src->is_tail;
- __pyx_v_dest->_is_tail = __pyx_t_4;
+ __pyx_v_dest->_is_tail = __pyx_v_src->is_tail;
- /* "pysam/csamtools.pyx":186
+ /* "csamtools.pyx":186
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail
* return dest # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.makePileupRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.makePileupRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":188
+/* "csamtools.pyx":188
* return dest
*
* cdef convertBinaryTagToList( uint8_t * s ): # <<<<<<<<<<<<<<
* cdef char auxtype
*/
-static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
+static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
char __pyx_v_auxtype;
uint8_t __pyx_v_byte_size;
int32_t __pyx_v_nvalues;
PyObject *__pyx_v_values = NULL;
- CYTHON_UNUSED long __pyx_v_x;
+ long __pyx_v_x;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("convertBinaryTagToList", 0);
+ __Pyx_RefNannySetupContext("convertBinaryTagToList");
__Pyx_TraceCall("convertBinaryTagToList", __pyx_f[0], 188);
- /* "pysam/csamtools.pyx":195
+ /* "csamtools.pyx":195
*
* # get byte size
* auxtype = s[0] # <<<<<<<<<<<<<<
*/
__pyx_v_auxtype = (__pyx_v_s[0]);
- /* "pysam/csamtools.pyx":196
+ /* "csamtools.pyx":196
* # get byte size
* auxtype = s[0]
* byte_size = bam_aux_type2size( auxtype ) # <<<<<<<<<<<<<<
*/
__pyx_v_byte_size = bam_aux_type2size(__pyx_v_auxtype);
- /* "pysam/csamtools.pyx":197
+ /* "csamtools.pyx":197
* auxtype = s[0]
* byte_size = bam_aux_type2size( auxtype )
* s += 1 # <<<<<<<<<<<<<<
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "pysam/csamtools.pyx":199
+ /* "csamtools.pyx":199
* s += 1
* # get number of values in array
* nvalues = (<int32_t*>s)[0] # <<<<<<<<<<<<<<
*/
__pyx_v_nvalues = (((int32_t *)__pyx_v_s)[0]);
- /* "pysam/csamtools.pyx":200
+ /* "csamtools.pyx":200
* # get number of values in array
* nvalues = (<int32_t*>s)[0]
* s += 4 # <<<<<<<<<<<<<<
*/
__pyx_v_s = (__pyx_v_s + 4);
- /* "pysam/csamtools.pyx":202
+ /* "csamtools.pyx":202
* s += 4
* # get values
* values = [] # <<<<<<<<<<<<<<
* for x from 0 <= x < nvalues:
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_values = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":203
+ /* "csamtools.pyx":203
* # get values
* values = []
* if auxtype == 'c': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 'c');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":204
+ /* "csamtools.pyx":204
* values = []
* if auxtype == 'c':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":205
+ /* "csamtools.pyx":205
* if auxtype == 'c':
* for x from 0 <= x < nvalues:
* values.append((<int8_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype == 'C':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_int8_t((((int8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":206
+ /* "csamtools.pyx":206
* for x from 0 <= x < nvalues:
* values.append((<int8_t*>s)[0])
* s += 1 # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":207
+ /* "csamtools.pyx":207
* values.append((<int8_t*>s)[0])
* s += 1
* elif auxtype == 'C': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 'C');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":208
+ /* "csamtools.pyx":208
* s += 1
* elif auxtype == 'C':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":209
+ /* "csamtools.pyx":209
* elif auxtype == 'C':
* for x from 0 <= x < nvalues:
* values.append((<uint8_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype == 's':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((((uint8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":210
+ /* "csamtools.pyx":210
* for x from 0 <= x < nvalues:
* values.append((<uint8_t*>s)[0])
* s += 1 # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":211
+ /* "csamtools.pyx":211
* values.append((<uint8_t*>s)[0])
* s += 1
* elif auxtype == 's': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 's');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":212
+ /* "csamtools.pyx":212
* s += 1
* elif auxtype == 's':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":213
+ /* "csamtools.pyx":213
* elif auxtype == 's':
* for x from 0 <= x < nvalues:
* values.append((<int16_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype == 'S':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":214
+ /* "csamtools.pyx":214
* for x from 0 <= x < nvalues:
* values.append((<int16_t*>s)[0])
* s += 2 # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":215
+ /* "csamtools.pyx":215
* values.append((<int16_t*>s)[0])
* s += 2
* elif auxtype == 'S': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 'S');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":216
+ /* "csamtools.pyx":216
* s += 2
* elif auxtype == 'S':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":217
+ /* "csamtools.pyx":217
* elif auxtype == 'S':
* for x from 0 <= x < nvalues:
* values.append((<uint16_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype == 'i':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":218
+ /* "csamtools.pyx":218
* for x from 0 <= x < nvalues:
* values.append((<uint16_t*>s)[0])
* s += 2 # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":219
+ /* "csamtools.pyx":219
* values.append((<uint16_t*>s)[0])
* s += 2
* elif auxtype == 'i': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 'i');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":220
+ /* "csamtools.pyx":220
* s += 2
* elif auxtype == 'i':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":221
+ /* "csamtools.pyx":221
* elif auxtype == 'i':
* for x from 0 <= x < nvalues:
* values.append((<int32_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'I':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_int32_t((((int32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":222
+ /* "csamtools.pyx":222
* for x from 0 <= x < nvalues:
* values.append((<int32_t*>s)[0])
* s += 4 # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":223
+ /* "csamtools.pyx":223
* values.append((<int32_t*>s)[0])
* s += 4
* elif auxtype == 'I': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 'I');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":224
+ /* "csamtools.pyx":224
* s += 4
* elif auxtype == 'I':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":225
+ /* "csamtools.pyx":225
* elif auxtype == 'I':
* for x from 0 <= x < nvalues:
* values.append((<uint32_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'f':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_uint32_t((((uint32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":226
+ /* "csamtools.pyx":226
* for x from 0 <= x < nvalues:
* values.append((<uint32_t*>s)[0])
* s += 4 # <<<<<<<<<<<<<<
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":227
+ /* "csamtools.pyx":227
* values.append((<uint32_t*>s)[0])
* s += 4
* elif auxtype == 'f': # <<<<<<<<<<<<<<
__pyx_t_2 = (__pyx_v_auxtype == 'f');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":228
+ /* "csamtools.pyx":228
* s += 4
* elif auxtype == 'f':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":229
+ /* "csamtools.pyx":229
* elif auxtype == 'f':
* for x from 0 <= x < nvalues:
* values.append((<float*>s)[0]) # <<<<<<<<<<<<<<
* s += 4
*
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyFloat_FromDouble((((float *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":230
+ /* "csamtools.pyx":230
* for x from 0 <= x < nvalues:
* values.append((<float*>s)[0])
* s += 4 # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":232
+ /* "csamtools.pyx":232
* s += 4
*
* return byte_size, nvalues, values # <<<<<<<<<<<<<<
__pyx_t_5 = __Pyx_PyInt_to_py_int32_t(__pyx_v_nvalues); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("pysam.csamtools.convertBinaryTagToList", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.convertBinaryTagToList", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_values);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":239
+/* "csamtools.pyx":239
* ## Generic callbacks for inserting python callbacks.
* #####################################################################
* cdef int fetch_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_f_5pysam_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
PyObject *__pyx_v_a = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch_callback", 0);
+ __Pyx_RefNannySetupContext("fetch_callback");
__Pyx_TraceCall("fetch_callback", __pyx_f[0], 239);
- /* "pysam/csamtools.pyx":244
+ /* "csamtools.pyx":244
* calls function in *f* with a new :class:`AlignedRead` object as parameter.
* '''
* a = makeAlignedRead( alignment ) # <<<<<<<<<<<<<<
* (<object>f)(a)
*
*/
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_alignment); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_alignment); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_a = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":245
+ /* "csamtools.pyx":245
* '''
* a = makeAlignedRead( alignment )
* (<object>f)(a) # <<<<<<<<<<<<<<
* class PileupColumn(object):
*/
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_a);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_a);
__Pyx_GIVEREF(__pyx_v_a);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_WriteUnraisable("pysam.csamtools.fetch_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.fetch_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_a);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_12PileupColumn_1__str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12PileupColumn_1__str__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12PileupColumn___str__)};
-static PyObject *__pyx_pw_5pysam_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_12PileupColumn___str__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":260
+/* "csamtools.pyx":260
* list of reads (:class:`pysam.PileupRead`) aligned to this column
* '''
* def __str__(self): # <<<<<<<<<<<<<<
* "\n" + "\n".join( map(str, self.pileups) )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn___str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pf_9csamtools_12PileupColumn___str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)};
+static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 260);
+ __pyx_self = __pyx_self;
- /* "pysam/csamtools.pyx":261
+ /* "csamtools.pyx":261
* '''
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
- /* "pysam/csamtools.pyx":262
+ /* "csamtools.pyx":262
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":261
+ /* "csamtools.pyx":261
* '''
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
__pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":262
+ /* "csamtools.pyx":262
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("pysam.csamtools.PileupColumn.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupColumn.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":264
+/* "csamtools.pyx":264
* "\n" + "\n".join( map(str, self.pileups) )
*
* cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_f_5pysam_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __pyx_v_pos, int __pyx_v_n, bam_pileup1_t *__pyx_v_pl, void *__pyx_v_f) {
+static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __pyx_v_pos, int __pyx_v_n, bam_pileup1_t *__pyx_v_pl, void *__pyx_v_f) {
PyObject *__pyx_v_p = NULL;
PyObject *__pyx_v_pileups = NULL;
int __pyx_v_x;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_callback", 0);
+ __Pyx_RefNannySetupContext("pileup_callback");
__Pyx_TraceCall("pileup_callback", __pyx_f[0], 264);
- /* "pysam/csamtools.pyx":281
+ /* "csamtools.pyx":281
* '''
*
* p = PileupColumn() # <<<<<<<<<<<<<<
__pyx_v_p = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":282
+ /* "csamtools.pyx":282
*
* p = PileupColumn()
* p.tid = tid # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__tid, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":283
+ /* "csamtools.pyx":283
* p = PileupColumn()
* p.tid = tid
* p.pos = pos # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pos, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":284
+ /* "csamtools.pyx":284
* p.tid = tid
* p.pos = pos
* p.n = n # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__n, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":285
+ /* "csamtools.pyx":285
* p.pos = pos
* p.n = n
* pileups = [] # <<<<<<<<<<<<<<
* cdef int x
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_pileups = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":288
+ /* "csamtools.pyx":288
*
* cdef int x
* for x from 0 <= x < n: # <<<<<<<<<<<<<<
__pyx_t_3 = __pyx_v_n;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":289
+ /* "csamtools.pyx":289
* cdef int x
* for x from 0 <= x < n:
* pileups.append( makePileupRead( &(pl[x]) ) ) # <<<<<<<<<<<<<<
* p.pileups = pileups
*
*/
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_pileups) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- /* "pysam/csamtools.pyx":290
+ /* "csamtools.pyx":290
* for x from 0 <= x < n:
* pileups.append( makePileupRead( &(pl[x]) ) )
* p.pileups = pileups # <<<<<<<<<<<<<<
*/
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pileups, ((PyObject *)__pyx_v_pileups)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":292
+ /* "csamtools.pyx":292
* p.pileups = pileups
*
* (<object>f)(p) # <<<<<<<<<<<<<<
* cdef int pileup_fetch_callback( bam1_t *b, void *data):
*/
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_p);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_p);
__Pyx_GIVEREF(__pyx_v_p);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_WriteUnraisable("pysam.csamtools.pileup_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.pileup_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_p);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":294
+/* "csamtools.pyx":294
* (<object>f)(p)
*
* cdef int pileup_fetch_callback( bam1_t *b, void *data): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_f_5pysam_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__pyx_v_data) {
+static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__pyx_v_data) {
bam_plbuf_t *__pyx_v_buf;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_fetch_callback", 0);
+ __Pyx_RefNannySetupContext("pileup_fetch_callback");
__Pyx_TraceCall("pileup_fetch_callback", __pyx_f[0], 294);
- /* "pysam/csamtools.pyx":300
+ /* "csamtools.pyx":300
* '''
* cdef bam_plbuf_t * buf
* buf = <bam_plbuf_t*>data # <<<<<<<<<<<<<<
*/
__pyx_v_buf = ((bam_plbuf_t *)__pyx_v_data);
- /* "pysam/csamtools.pyx":301
+ /* "csamtools.pyx":301
* cdef bam_plbuf_t * buf
* buf = <bam_plbuf_t*>data
* bam_plbuf_push(b, buf) # <<<<<<<<<<<<<<
*/
bam_plbuf_push(__pyx_v_b, __pyx_v_buf);
- /* "pysam/csamtools.pyx":302
+ /* "csamtools.pyx":302
* buf = <bam_plbuf_t*>data
* bam_plbuf_push(b, buf)
* return 0 # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore___init__)};
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore___init__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":308
+/* "csamtools.pyx":308
* stderr is captured.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___init__)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 308);
+ __pyx_self = __pyx_self;
- /* "pysam/csamtools.pyx":309
+ /* "csamtools.pyx":309
* '''
* def __init__(self):
* return # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11StderrStore_2readAndRelease[] = "StderrStore.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore_2readAndRelease)};
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":314
+/* "csamtools.pyx":314
* self.stderr_save.setfd( self.stderr_h )
*
* def readAndRelease( self ): # <<<<<<<<<<<<<<
* self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_1readAndRelease[] = "StderrStore.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_1readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_1readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_1readAndRelease)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease", 0);
+ __Pyx_RefNannySetupContext("readAndRelease");
__Pyx_TraceCall("readAndRelease", __pyx_f[0], 314);
+ __pyx_self = __pyx_self;
- /* "pysam/csamtools.pyx":315
+ /* "csamtools.pyx":315
*
* def readAndRelease( self ):
* return [] # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.StderrStore.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.StderrStore.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11StderrStore_4release[] = "StderrStore.release(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore_4release)};
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("release (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore_4release(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":323
+/* "csamtools.pyx":323
* return lines
*
* def release(self): # <<<<<<<<<<<<<<
* self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_2release[] = "StderrStore.release(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_2release)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release", 0);
+ __Pyx_RefNannySetupContext("release");
__Pyx_TraceCall("release", __pyx_f[0], 323);
+ __pyx_self = __pyx_self;
- /* "pysam/csamtools.pyx":324
+ /* "csamtools.pyx":324
*
* def release(self):
* return # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11StderrStore_6__del__[] = "StderrStore.__del__(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_7__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_7__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore_6__del__)};
-static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":329
+/* "csamtools.pyx":329
* os.remove( self.stderr_f )
*
* def __del__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_3__del__[] = "StderrStore.__del__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_3__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_3__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_3__del__)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__del__", 0);
+ __Pyx_RefNannySetupContext("__del__");
__Pyx_TraceCall("__del__", __pyx_f[0], 329);
+ __pyx_self = __pyx_self;
- /* "pysam/csamtools.pyx":330
+ /* "csamtools.pyx":330
*
* def __del__(self):
* self.release() # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.StderrStore.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.StderrStore.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18StderrStoreWindows___init__)};
-static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":334
+/* "csamtools.pyx":334
* class StderrStoreWindows():
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass # <<<<<<<<<<<<<<
* def release(self): pass
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows___init__)};
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 334);
+ __pyx_self = __pyx_self;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease)};
-static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":335
+/* "csamtools.pyx":335
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
* def readAndRelease(self): return [] # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows_1readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_1readAndRelease)};
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease", 0);
+ __Pyx_RefNannySetupContext("readAndRelease");
__Pyx_TraceCall("readAndRelease", __pyx_f[0], 335);
+ __pyx_self = __pyx_self;
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.StderrStoreWindows.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.StderrStoreWindows.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_18StderrStoreWindows_4release[] = "StderrStoreWindows.release(self)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18StderrStoreWindows_4release)};
-static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("release (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":336
+/* "csamtools.pyx":336
* def __init__(self): pass
* def readAndRelease(self): return []
* def release(self): pass # <<<<<<<<<<<<<<
* if platform.system()=='Windows':
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows_2release[] = "StderrStoreWindows.release(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_2release)};
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release", 0);
+ __Pyx_RefNannySetupContext("release");
__Pyx_TraceCall("release", __pyx_f[0], 336);
+ __pyx_self = __pyx_self;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
- __Pyx_XDECREF(__pyx_v_args);
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":387
+/* "csamtools.pyx":387
* '''
*
* def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
* self._filename = NULL
*/
-static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
+static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_RefNannySetupContext("__cinit__");
__Pyx_TraceCall("__cinit__", __pyx_f[0], 387);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
- /* "pysam/csamtools.pyx":388
+ /* "csamtools.pyx":388
*
* def __cinit__(self, *args, **kwargs ):
* self.fastafile = NULL # <<<<<<<<<<<<<<
* self._filename = NULL
* self._open( *args, **kwargs )
*/
- __pyx_v_self->fastafile = NULL;
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
- /* "pysam/csamtools.pyx":389
+ /* "csamtools.pyx":389
* def __cinit__(self, *args, **kwargs ):
* self.fastafile = NULL
* self._filename = NULL # <<<<<<<<<<<<<<
* self._open( *args, **kwargs )
*
*/
- __pyx_v_self->_filename = NULL;
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = NULL;
- /* "pysam/csamtools.pyx":390
+ /* "csamtools.pyx":390
* self.fastafile = NULL
* self._filename = NULL
* self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
*
* def _isOpen( self ):
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_r = 0;
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_9Fastafile_2_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":392
+/* "csamtools.pyx":392
* self._open( *args, **kwargs )
*
* def _isOpen( self ): # <<<<<<<<<<<<<<
* return self.fastafile != NULL
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_1_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen", 0);
+ __Pyx_RefNannySetupContext("_isOpen");
__Pyx_TraceCall("_isOpen", __pyx_f[0], 392);
- /* "pysam/csamtools.pyx":394
+ /* "csamtools.pyx":394
* def _isOpen( self ):
* '''return true if samfile has been opened.'''
* return self.fastafile != NULL # <<<<<<<<<<<<<<
* def __len__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static Py_ssize_t __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self); /*proto*/
-static Py_ssize_t __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self) {
- Py_ssize_t __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":396
+/* "csamtools.pyx":396
* return self.fastafile != NULL
*
* def __len__(self): # <<<<<<<<<<<<<<
* raise ValueError( "calling len() on closed file" )
*/
-static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
+static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self); /*proto*/
+static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__len__", 0);
+ __Pyx_RefNannySetupContext("__len__");
__Pyx_TraceCall("__len__", __pyx_f[0], 396);
- /* "pysam/csamtools.pyx":397
+ /* "csamtools.pyx":397
*
* def __len__(self):
* if self.fastafile == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "calling len() on closed file" )
*
*/
- __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":398
+ /* "csamtools.pyx":398
* def __len__(self):
* if self.fastafile == NULL:
* raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":400
+ /* "csamtools.pyx":400
* raise ValueError( "calling len() on closed file" )
*
* return faidx_fetch_nseq(self.fastafile) # <<<<<<<<<<<<<<
*
* def _open( self,
*/
- __pyx_r = faidx_fetch_nseq(__pyx_v_self->fastafile);
+ __pyx_r = faidx_fetch_nseq(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
goto __pyx_L0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_9Fastafile_6_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_open (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_6_open(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self), ((PyObject *)__pyx_v_filename));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":402
+/* "csamtools.pyx":402
* return faidx_fetch_nseq(self.fastafile)
*
* def _open( self, # <<<<<<<<<<<<<<
* '''open an indexed fasta file.
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_3_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open", 0);
+ __Pyx_RefNannySetupContext("_open");
__Pyx_TraceCall("_open", __pyx_f[0], 402);
__Pyx_INCREF(__pyx_v_filename);
- /* "pysam/csamtools.pyx":410
+ /* "csamtools.pyx":410
*
* # close a previously opened file
* if self.fastafile != NULL: self.close() # <<<<<<<<<<<<<<
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename)
*/
- __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
if (__pyx_t_1) {
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":411
+ /* "csamtools.pyx":411
* # close a previously opened file
* if self.fastafile != NULL: self.close()
* if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename)
*/
- __pyx_t_1 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_1) {
- free(__pyx_v_self->_filename);
- goto __pyx_L4;
+ free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":412
+ /* "csamtools.pyx":412
* if self.fastafile != NULL: self.close()
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<<
* self._filename = strdup(filename)
* self.fastafile = fai_load( filename )
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_v_filename);
__pyx_v_filename = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":413
+ /* "csamtools.pyx":413
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename) # <<<<<<<<<<<<<<
*
*/
__pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_filename = strdup(__pyx_t_4);
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = strdup(__pyx_t_4);
- /* "pysam/csamtools.pyx":414
+ /* "csamtools.pyx":414
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename)
* self.fastafile = fai_load( filename ) # <<<<<<<<<<<<<<
* if self.fastafile == NULL:
*/
__pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fastafile = fai_load(__pyx_t_4);
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = fai_load(__pyx_t_4);
- /* "pysam/csamtools.pyx":416
+ /* "csamtools.pyx":416
* self.fastafile = fai_load( filename )
*
* if self.fastafile == NULL: # <<<<<<<<<<<<<<
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":417
+ /* "csamtools.pyx":417
*
* if self.fastafile == NULL:
* raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
__pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_3));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
__pyx_t_3 = 0;
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_filename);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_9Fastafile_8close[] = "Fastafile.close(self)";
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("close (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_8close(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":419
+/* "csamtools.pyx":419
* raise IOError("could not open file `%s`" % filename )
*
* def close( self ): # <<<<<<<<<<<<<<
* fai_destroy( self.fastafile )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_4close[] = "Fastafile.close(self)";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_RefNannySetupContext("close");
__Pyx_TraceCall("close", __pyx_f[0], 419);
- /* "pysam/csamtools.pyx":420
+ /* "csamtools.pyx":420
*
* def close( self ):
* if self.fastafile != NULL: # <<<<<<<<<<<<<<
* fai_destroy( self.fastafile )
* self.fastafile = NULL
*/
- __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":421
+ /* "csamtools.pyx":421
* def close( self ):
* if self.fastafile != NULL:
* fai_destroy( self.fastafile ) # <<<<<<<<<<<<<<
* self.fastafile = NULL
*
*/
- fai_destroy(__pyx_v_self->fastafile);
+ fai_destroy(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
- /* "pysam/csamtools.pyx":422
+ /* "csamtools.pyx":422
* if self.fastafile != NULL:
* fai_destroy( self.fastafile )
* self.fastafile = NULL # <<<<<<<<<<<<<<
*
* def __dealloc__(self):
*/
- __pyx_v_self->fastafile = NULL;
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":424
+/* "csamtools.pyx":424
* self.fastafile = NULL
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
* if self._filename != NULL: free(self._filename)
*/
-static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
+static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 424);
- /* "pysam/csamtools.pyx":425
+ /* "csamtools.pyx":425
*
* def __dealloc__(self):
* self.close() # <<<<<<<<<<<<<<
* if self._filename != NULL: free(self._filename)
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":426
+ /* "csamtools.pyx":426
* def __dealloc__(self):
* self.close()
* if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
*
* property filename:
*/
- __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_3) {
- free(__pyx_v_self->_filename);
- goto __pyx_L3;
+ free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":430
+/* "csamtools.pyx":430
* property filename:
* '''number of :term:`filename` associated with this object.'''
* def __get__(self): # <<<<<<<<<<<<<<
* return self._filename
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 430);
- /* "pysam/csamtools.pyx":431
+ /* "csamtools.pyx":431
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self._filename
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":432
+ /* "csamtools.pyx":432
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return self._filename # <<<<<<<<<<<<<<
* def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_9Fastafile_12fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* is given and *start* is None, the sequence from the\n first base is returned. Similarly, if *end* is None, the sequence\n until the last base is returned.\n\n Alternatively, a samtools :term:`region` string can be supplied.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":434
+ * return self._filename
+ *
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_6fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* is given and *start* is None, the sequence from the\n first base is returned. Similarly, if *end* is None, the sequence\n until the last base is returned.\n\n Alternatively, a samtools :term:`region` string can be supplied.\n ";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- PyObject *__pyx_r = 0;
+ int __pyx_v_length;
+ char *__pyx_v_seq;
+ PyObject *__pyx_v_py_seq = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch");
+ __Pyx_TraceCall("fetch", __pyx_f[0], 434);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[4] = {0,0,0,0};
- /* "pysam/csamtools.pyx":435
+ /* "csamtools.pyx":435
*
* def fetch( self,
* reference = None, # <<<<<<<<<<<<<<
*/
values[0] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":436
+ /* "csamtools.pyx":436
* def fetch( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":437
+ /* "csamtools.pyx":437
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
*/
values[2] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":438
+ /* "csamtools.pyx":438
* start = None,
* end = None,
* region = None): # <<<<<<<<<<<<<<
values[3] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":434
- * return self._filename
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
- int __pyx_v_length;
- char *__pyx_v_seq;
- PyObject *__pyx_v_py_seq = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch", 0);
- __Pyx_TraceCall("fetch", __pyx_f[0], 434);
__Pyx_INCREF(__pyx_v_start);
__Pyx_INCREF(__pyx_v_end);
__Pyx_INCREF(__pyx_v_region);
- /* "pysam/csamtools.pyx":455
+ /* "csamtools.pyx":455
* '''
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":456
+ /* "csamtools.pyx":456
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":461
+ /* "csamtools.pyx":461
* cdef char * seq
*
* if not region: # <<<<<<<<<<<<<<
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":462
+ /* "csamtools.pyx":462
*
* if not region:
* if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L8;
}
- __pyx_L5:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":463
+ /* "csamtools.pyx":463
* if not region:
* if reference is None: raise ValueError( 'no sequence/region supplied.' )
* if start is None: start = 0 # <<<<<<<<<<<<<<
__Pyx_INCREF(__pyx_int_0);
__Pyx_DECREF(__pyx_v_start);
__pyx_v_start = __pyx_int_0;
- goto __pyx_L6;
+ goto __pyx_L9;
}
- __pyx_L6:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":464
+ /* "csamtools.pyx":464
* if reference is None: raise ValueError( 'no sequence/region supplied.' )
* if start is None: start = 0
* if end is None: end = max_pos -1 # <<<<<<<<<<<<<<
*/
__pyx_t_3 = (__pyx_v_end == Py_None);
if (__pyx_t_3) {
- __pyx_t_2 = PyInt_FromLong((__pyx_v_5pysam_9csamtools_max_pos - 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong((__pyx_v_9csamtools_max_pos - 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_end);
__pyx_v_end = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":466
+ /* "csamtools.pyx":466
* if end is None: end = max_pos -1
*
* if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) # <<<<<<<<<<<<<<
* if start == end: return b""
* # valid ranges are from 0 to 2^29-1
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_start);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start);
__Pyx_GIVEREF(__pyx_v_start);
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
- /* "pysam/csamtools.pyx":467
+ /* "csamtools.pyx":467
*
* if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
* if start == end: return b"" # <<<<<<<<<<<<<<
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
__Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
- /* "pysam/csamtools.pyx":469
+ /* "csamtools.pyx":469
* if start == end: return b""
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
* if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end )
* # note: faidx_fetch_seq has a bug such that out-of-range access
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_5pysam_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ goto __pyx_L13;
}
- __pyx_L10:;
+ __pyx_L13:;
- /* "pysam/csamtools.pyx":470
+ /* "csamtools.pyx":470
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
* if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
* # note: faidx_fetch_seq has a bug such that out-of-range access
* # always returns the last residue. Hence do not use faidx_fetch_seq,
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_5pysam_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ goto __pyx_L14;
}
- __pyx_L11:;
+ __pyx_L14:;
- /* "pysam/csamtools.pyx":479
+ /* "csamtools.pyx":479
* # end-1,
* # &length)
* region = "%s:%i-%i" % (reference, start+1, end) # <<<<<<<<<<<<<<
__pyx_t_1 = PyNumber_Add(__pyx_v_start, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
__pyx_v_region = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":480
+ /* "csamtools.pyx":480
* # &length)
* region = "%s:%i-%i" % (reference, start+1, end)
* if PY_MAJOR_VERSION >= 3: # <<<<<<<<<<<<<<
__pyx_t_3 = (PY_MAJOR_VERSION >= 3);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":481
+ /* "csamtools.pyx":481
* region = "%s:%i-%i" % (reference, start+1, end)
* if PY_MAJOR_VERSION >= 3:
* region = region.encode('ascii') # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L12;
+ goto __pyx_L15;
}
- __pyx_L12:;
+ __pyx_L15:;
- /* "pysam/csamtools.pyx":483
+ /* "csamtools.pyx":483
* region = region.encode('ascii')
* seq = fai_fetch( self.fastafile,
* region, # <<<<<<<<<<<<<<
*/
__pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":484
+ /* "csamtools.pyx":484
* seq = fai_fetch( self.fastafile,
* region,
* &length ) # <<<<<<<<<<<<<<
* else:
* # samtools adds a '\0' at the end
*/
- __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
- goto __pyx_L4;
+ __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
+ goto __pyx_L7;
}
/*else*/ {
- /* "pysam/csamtools.pyx":487
+ /* "csamtools.pyx":487
* else:
* # samtools adds a '\0' at the end
* seq = fai_fetch( self.fastafile, region, &length ) # <<<<<<<<<<<<<<
* # copy to python
*/
__pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
+ __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
}
- __pyx_L4:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":490
+ /* "csamtools.pyx":490
*
* # copy to python
* if seq == NULL: # <<<<<<<<<<<<<<
__pyx_t_3 = (__pyx_v_seq == NULL);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":491
+ /* "csamtools.pyx":491
* # copy to python
* if seq == NULL:
* return b"" # <<<<<<<<<<<<<<
__Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L13;
+ goto __pyx_L16;
}
/*else*/ {
- /* "pysam/csamtools.pyx":493
+ /* "csamtools.pyx":493
* return b""
* else:
* try: # <<<<<<<<<<<<<<
*/
/*try:*/ {
- /* "pysam/csamtools.pyx":494
+ /* "csamtools.pyx":494
* else:
* try:
* py_seq = seq[:length] # <<<<<<<<<<<<<<
* finally:
* free(seq)
*/
- __pyx_t_2 = PyBytes_FromStringAndSize(((const char*)__pyx_v_seq) + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L15;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L18;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_py_seq = __pyx_t_2;
__pyx_t_2 = 0;
}
- /* "pysam/csamtools.pyx":496
+ /* "csamtools.pyx":496
* py_seq = seq[:length]
* finally:
* free(seq) # <<<<<<<<<<<<<<
PyObject *__pyx_exc_type, *__pyx_exc_value, *__pyx_exc_tb;
int __pyx_exc_lineno;
__pyx_exc_type = 0; __pyx_exc_value = 0; __pyx_exc_tb = 0; __pyx_exc_lineno = 0;
- __pyx_why = 0; goto __pyx_L16;
- __pyx_L15: {
+ __pyx_why = 0; goto __pyx_L19;
+ __pyx_L18: {
__pyx_why = 4;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_ErrFetch(&__pyx_exc_type, &__pyx_exc_value, &__pyx_exc_tb);
__pyx_exc_lineno = __pyx_lineno;
- goto __pyx_L16;
+ goto __pyx_L19;
}
- __pyx_L16:;
+ __pyx_L19:;
free(__pyx_v_seq);
switch (__pyx_why) {
case 4: {
}
}
}
- __pyx_L13:;
+ __pyx_L16:;
- /* "pysam/csamtools.pyx":498
+ /* "csamtools.pyx":498
* free(seq)
*
* return py_seq # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_py_seq);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":500
+/* "csamtools.pyx":500
* return py_seq
*
* cdef char * _fetch( self, char * reference, int start, int end, int * length ): # <<<<<<<<<<<<<<
*
*/
-static char *__pyx_f_5pysam_9csamtools_9Fastafile__fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, char *__pyx_v_reference, int __pyx_v_start, int __pyx_v_end, int *__pyx_v_length) {
+static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, char *__pyx_v_reference, int __pyx_v_start, int __pyx_v_end, int *__pyx_v_length) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_fetch", 0);
+ __Pyx_RefNannySetupContext("_fetch");
__Pyx_TraceCall("_fetch", __pyx_f[0], 500);
- /* "pysam/csamtools.pyx":507
+ /* "csamtools.pyx":507
* start,
* end-1,
* length ) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":512
+/* "csamtools.pyx":512
* #------------------------------------------------------------------------
* #------------------------------------------------------------------------
* cdef int count_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
* '''
*/
-static int __pyx_f_5pysam_9csamtools_count_callback(CYTHON_UNUSED bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
int *__pyx_v_counter;
int __pyx_r;
__Pyx_RefNannyDeclarations
long __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count_callback", 0);
+ __Pyx_RefNannySetupContext("count_callback");
__Pyx_TraceCall("count_callback", __pyx_f[0], 512);
- /* "pysam/csamtools.pyx":515
+ /* "csamtools.pyx":515
* '''callback for bam_fetch - count number of reads.
* '''
* cdef int* counter = (<int*>f) # <<<<<<<<<<<<<<
*/
__pyx_v_counter = ((int *)__pyx_v_f);
- /* "pysam/csamtools.pyx":516
+ /* "csamtools.pyx":516
* '''
* cdef int* counter = (<int*>f)
* counter[0] += 1; # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":526
+/* "csamtools.pyx":526
* #------------------------------------------------------------------------
* #------------------------------------------------------------------------
* cdef int mate_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
* '''
*/
-static int __pyx_f_5pysam_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
- __pyx_t_5pysam_9csamtools_MateData *__pyx_v_d;
+static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+ __pyx_t_9csamtools_MateData *__pyx_v_d;
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate_callback", 0);
+ __Pyx_RefNannySetupContext("mate_callback");
__Pyx_TraceCall("mate_callback", __pyx_f[0], 526);
- /* "pysam/csamtools.pyx":529
+ /* "csamtools.pyx":529
* '''callback for bam_fetch = filter mate
* '''
* cdef MateData * d = (<MateData*>f) # <<<<<<<<<<<<<<
* # printf("mate = %p, name1 = %s, name2=%s\t%i\t%i\t%i\n",
* # d.mate, d.name, bam1_qname(alignment),
*/
- __pyx_v_d = ((__pyx_t_5pysam_9csamtools_MateData *)__pyx_v_f);
+ __pyx_v_d = ((__pyx_t_9csamtools_MateData *)__pyx_v_f);
- /* "pysam/csamtools.pyx":534
+ /* "csamtools.pyx":534
* # d.flag, alignment.core.flag, alignment.core.flag & d.flag)
*
* if d.mate == NULL: # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_d->mate == NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":540
+ /* "csamtools.pyx":540
* # also, make sure that we get the other read by comparing
* # the flags
* if alignment.core.flag & d.flag != 0 and \ # <<<<<<<<<<<<<<
__pyx_t_1 = ((__pyx_v_alignment->core.flag & __pyx_v_d->flag) != 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":541
+ /* "csamtools.pyx":541
* # the flags
* if alignment.core.flag & d.flag != 0 and \
* strcmp( bam1_qname( alignment ), d.name ) == 0: # <<<<<<<<<<<<<<
}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":542
+ /* "csamtools.pyx":542
* if alignment.core.flag & d.flag != 0 and \
* strcmp( bam1_qname( alignment ), d.name ) == 0:
* d.mate = bam_dup1( alignment ) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
- __Pyx_XDECREF(__pyx_v_args);
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":592
+/* "csamtools.pyx":592
* '''
*
* def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
* self._filename = NULL
*/
-static int __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
+static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_RefNannySetupContext("__cinit__");
__Pyx_TraceCall("__cinit__", __pyx_f[0], 592);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
- /* "pysam/csamtools.pyx":593
+ /* "csamtools.pyx":593
*
* def __cinit__(self, *args, **kwargs ):
* self.samfile = NULL # <<<<<<<<<<<<<<
* self._filename = NULL
* self.isbam = False
*/
- __pyx_v_self->samfile = NULL;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
- /* "pysam/csamtools.pyx":594
+ /* "csamtools.pyx":594
* def __cinit__(self, *args, **kwargs ):
* self.samfile = NULL
* self._filename = NULL # <<<<<<<<<<<<<<
* self.isbam = False
* self.isstream = False
*/
- __pyx_v_self->_filename = NULL;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = NULL;
- /* "pysam/csamtools.pyx":595
+ /* "csamtools.pyx":595
* self.samfile = NULL
* self._filename = NULL
* self.isbam = False # <<<<<<<<<<<<<<
* self.isstream = False
* self._open( *args, **kwargs )
*/
- __pyx_v_self->isbam = 0;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = 0;
- /* "pysam/csamtools.pyx":596
+ /* "csamtools.pyx":596
* self._filename = NULL
* self.isbam = False
* self.isstream = False # <<<<<<<<<<<<<<
* self._open( *args, **kwargs )
*
*/
- __pyx_v_self->isstream = 0;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = 0;
- /* "pysam/csamtools.pyx":597
+ /* "csamtools.pyx":597
* self.isbam = False
* self.isstream = False
* self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
*
* # allocate memory for iterator
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":600
+ /* "csamtools.pyx":600
*
* # allocate memory for iterator
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
* def _isOpen( self ):
*/
- __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
__pyx_r = 0;
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_2_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":602
+/* "csamtools.pyx":602
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
* def _isOpen( self ): # <<<<<<<<<<<<<<
* return self.samfile != NULL
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_1_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen", 0);
+ __Pyx_RefNannySetupContext("_isOpen");
__Pyx_TraceCall("_isOpen", __pyx_f[0], 602);
- /* "pysam/csamtools.pyx":604
+ /* "csamtools.pyx":604
* def _isOpen( self ):
* '''return true if samfile has been opened.'''
* return self.samfile != NULL # <<<<<<<<<<<<<<
* def _hasIndex( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.Samfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_4_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_hasIndex (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":606
+/* "csamtools.pyx":606
* return self.samfile != NULL
*
* def _hasIndex( self ): # <<<<<<<<<<<<<<
* return self.index != NULL
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_2_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_hasIndex", 0);
+ __Pyx_RefNannySetupContext("_hasIndex");
__Pyx_TraceCall("_hasIndex", __pyx_f[0], 606);
- /* "pysam/csamtools.pyx":608
+ /* "csamtools.pyx":608
* def _hasIndex( self ):
* '''return true if samfile has an existing (and opened) index.'''
* return self.index != NULL # <<<<<<<<<<<<<<
* def _open( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.Samfile._hasIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._hasIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_6_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":610
+ * return self.index != NULL
+ *
+ * def _open( self, # <<<<<<<<<<<<<<
+ * filename,
+ * mode = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_3_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_filename = 0;
PyObject *__pyx_v_mode = 0;
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template = 0;
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_template = 0;
PyObject *__pyx_v_referencenames = 0;
PyObject *__pyx_v_referencelengths = 0;
PyObject *__pyx_v_text = 0;
PyObject *__pyx_v_add_sq_text = 0;
PyObject *__pyx_v_check_header = 0;
PyObject *__pyx_v_check_sq = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_msg = NULL;
+ bam_header_t *__pyx_v_header_to_write;
+ PyObject *__pyx_v_bmode = 0;
+ char *__pyx_v_ctext;
+ PyObject *__pyx_v_n = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_name = NULL;
+ PyObject *__pyx_v_store = NULL;
+ PyObject *__pyx_v_ref = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_open (wrapper)", 0);
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_t_11;
+ char *__pyx_t_12;
+ Py_ssize_t __pyx_t_13;
+ Py_ssize_t __pyx_t_14;
+ PyObject *(*__pyx_t_15)(PyObject *);
+ size_t __pyx_t_16;
+ int32_t __pyx_t_17;
+ long __pyx_t_18;
+ uint32_t __pyx_t_19;
+ const char* __pyx_t_20;
+ int __pyx_t_21;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_open");
+ __Pyx_TraceCall("_open", __pyx_f[0], 610);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
PyObject* values[11] = {0,0,0,0,0,0,0,0,0,0,0};
- /* "pysam/csamtools.pyx":612
+ /* "csamtools.pyx":612
* def _open( self,
* filename,
* mode = None, # <<<<<<<<<<<<<<
*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":613
+ /* "csamtools.pyx":613
* filename,
* mode = None,
* Samfile template = None, # <<<<<<<<<<<<<<
* referencenames = None,
* referencelengths = None,
*/
- values[2] = (PyObject *)((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None);
+ values[2] = (PyObject *)((struct __pyx_obj_9csamtools_Samfile *)Py_None);
- /* "pysam/csamtools.pyx":614
+ /* "csamtools.pyx":614
* mode = None,
* Samfile template = None,
* referencenames = None, # <<<<<<<<<<<<<<
*/
values[3] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":615
+ /* "csamtools.pyx":615
* Samfile template = None,
* referencenames = None,
* referencelengths = None, # <<<<<<<<<<<<<<
*/
values[4] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":616
+ /* "csamtools.pyx":616
* referencenames = None,
* referencelengths = None,
* text = None, # <<<<<<<<<<<<<<
*/
values[5] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":617
+ /* "csamtools.pyx":617
* referencelengths = None,
* text = None,
* header = None, # <<<<<<<<<<<<<<
*/
values[6] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":618
+ /* "csamtools.pyx":618
* text = None,
* header = None,
* port = None, # <<<<<<<<<<<<<<
values[10] = __pyx_k_23;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 11: values[10] = PyTuple_GET_ITEM(__pyx_args, 10);
case 10: values[9] = PyTuple_GET_ITEM(__pyx_args, 9);
case 9: values[8] = PyTuple_GET_ITEM(__pyx_args, 8);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
}
__pyx_v_filename = values[0];
__pyx_v_mode = values[1];
- __pyx_v_template = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[2]);
+ __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)values[2]);
__pyx_v_referencenames = values[3];
__pyx_v_referencelengths = values[4];
__pyx_v_text = values[5];
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("_open", 0, 1, 11, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_6_open(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_template, __pyx_v_referencenames, __pyx_v_referencelengths, __pyx_v_text, __pyx_v_header, __pyx_v_port, __pyx_v_add_sq_text, __pyx_v_check_header, __pyx_v_check_sq);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":610
- * return self.index != NULL
- *
- * def _open( self, # <<<<<<<<<<<<<<
- * filename,
- * mode = None,
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq) {
- CYTHON_UNUSED PyObject *__pyx_v_msg = NULL;
- bam_header_t *__pyx_v_header_to_write;
- PyObject *__pyx_v_bmode = 0;
- char *__pyx_v_ctext;
- PyObject *__pyx_v_n = NULL;
- PyObject *__pyx_v_x = NULL;
- PyObject *__pyx_v_name = NULL;
- PyObject *__pyx_v_store = NULL;
- PyObject *__pyx_v_ref = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
- char *__pyx_t_12;
- Py_ssize_t __pyx_t_13;
- bam_header_t *__pyx_t_14;
- Py_ssize_t __pyx_t_15;
- PyObject *(*__pyx_t_16)(PyObject *);
- size_t __pyx_t_17;
- int32_t __pyx_t_18;
- long __pyx_t_19;
- uint32_t __pyx_t_20;
- const char* __pyx_t_21;
- int __pyx_t_22;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open", 0);
- __Pyx_TraceCall("_open", __pyx_f[0], 610);
__Pyx_INCREF(__pyx_v_filename);
__Pyx_INCREF(__pyx_v_referencenames);
__Pyx_INCREF(__pyx_v_text);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":630
+ /* "csamtools.pyx":630
*
* # read mode autodetection
* if mode is None: # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_mode == Py_None);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":631
+ /* "csamtools.pyx":631
* # read mode autodetection
* if mode is None:
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_4);
/*try:*/ {
- /* "pysam/csamtools.pyx":632
+ /* "csamtools.pyx":632
* if mode is None:
* try:
* self._open(filename, 'rb', template=template, # <<<<<<<<<<<<<<
* referencenames=referencenames,
* referencelengths=referencelengths,
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "pysam/csamtools.pyx":633
+ /* "csamtools.pyx":633
* try:
* self._open(filename, 'rb', template=template,
* referencenames=referencenames, # <<<<<<<<<<<<<<
* referencelengths=referencelengths,
* text=text, header=header, port=port,
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "pysam/csamtools.pyx":634
+ /* "csamtools.pyx":634
* self._open(filename, 'rb', template=template,
* referencenames=referencenames,
* referencelengths=referencelengths, # <<<<<<<<<<<<<<
* text=text, header=header, port=port,
* check_header=check_header,
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "pysam/csamtools.pyx":635
+ /* "csamtools.pyx":635
* referencenames=referencenames,
* referencelengths=referencelengths,
* text=text, header=header, port=port, # <<<<<<<<<<<<<<
* check_header=check_header,
* check_sq=check_sq)
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "pysam/csamtools.pyx":636
+ /* "csamtools.pyx":636
* referencelengths=referencelengths,
* text=text, header=header, port=port,
* check_header=check_header, # <<<<<<<<<<<<<<
* check_sq=check_sq)
* return
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- /* "pysam/csamtools.pyx":637
+ /* "csamtools.pyx":637
* text=text, header=header, port=port,
* check_header=check_header,
* check_sq=check_sq) # <<<<<<<<<<<<<<
* return
* except ValueError, msg:
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __pyx_t_8 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":638
+ /* "csamtools.pyx":638
* check_header=check_header,
* check_sq=check_sq)
* return # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L8_try_return;
+ goto __pyx_L11_try_return;
}
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L11_try_end;
- __pyx_L8_try_return:;
+ goto __pyx_L14_try_end;
+ __pyx_L11_try_return:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
goto __pyx_L0;
- __pyx_L4_error:;
+ __pyx_L7_error:;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":639
+ /* "csamtools.pyx":639
* check_sq=check_sq)
* return
* except ValueError, msg: # <<<<<<<<<<<<<<
*/
__pyx_t_9 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_9) {
- __Pyx_AddTraceback("pysam.csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L5_exception_handled;
+ goto __pyx_L8_exception_handled;
}
- __pyx_L6_except_error:;
+ __pyx_L9_except_error:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
goto __pyx_L1_error;
- __pyx_L5_exception_handled:;
+ __pyx_L8_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
- __pyx_L11_try_end:;
+ __pyx_L14_try_end:;
}
- /* "pysam/csamtools.pyx":642
+ /* "csamtools.pyx":642
* pass
*
* self._open(filename, 'r', template=template, # <<<<<<<<<<<<<<
* referencenames=referencenames,
* referencelengths=referencelengths,
*/
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":643
+ /* "csamtools.pyx":643
*
* self._open(filename, 'r', template=template,
* referencenames=referencenames, # <<<<<<<<<<<<<<
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":644
+ /* "csamtools.pyx":644
* self._open(filename, 'r', template=template,
* referencenames=referencenames,
* referencelengths=referencelengths, # <<<<<<<<<<<<<<
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":645
+ /* "csamtools.pyx":645
* referencenames=referencenames,
* referencelengths=referencelengths,
* text=text, header=header, port=port, # <<<<<<<<<<<<<<
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":646
+ /* "csamtools.pyx":646
* referencelengths=referencelengths,
* text=text, header=header, port=port,
* check_header=check_header, # <<<<<<<<<<<<<<
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":647
+ /* "csamtools.pyx":647
* text=text, header=header, port=port,
* check_header=check_header,
* check_sq=check_sq) # <<<<<<<<<<<<<<
*
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":648
+ /* "csamtools.pyx":648
* check_header=check_header,
* check_sq=check_sq)
* return # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":650
+ /* "csamtools.pyx":650
* return
*
* assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode # <<<<<<<<<<<<<<
#ifndef CYTHON_WITHOUT_ASSERTIONS
__Pyx_INCREF(__pyx_v_mode);
__pyx_t_5 = __pyx_v_mode;
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!((int)__pyx_t_1)) {
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((int)__pyx_t_10);
} else {
__pyx_t_11 = ((int)__pyx_t_1);
}
if (!__pyx_t_11) {
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__rb), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__rb), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((int)__pyx_t_1);
} else {
__pyx_t_10 = __pyx_t_11;
}
if (!__pyx_t_10) {
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__wb), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_11 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wb), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = ((int)__pyx_t_11);
} else {
__pyx_t_1 = __pyx_t_10;
}
if (!__pyx_t_1) {
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__wh), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wh), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((int)__pyx_t_10);
} else {
__pyx_t_11 = __pyx_t_1;
}
if (!__pyx_t_11) {
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__wbu), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wbu), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((int)__pyx_t_1);
} else {
__pyx_t_10 = __pyx_t_11;
}
if (!__pyx_t_10) {
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__rU), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_11 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__rU), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = ((int)__pyx_t_11);
} else {
__pyx_t_1 = __pyx_t_10;
}
#endif
- /* "pysam/csamtools.pyx":655
+ /* "csamtools.pyx":655
*
* # close a previously opened file
* if self.samfile != NULL: self.close() # <<<<<<<<<<<<<<
* self.samfile = NULL
*
*/
- __pyx_t_1 = (__pyx_v_self->samfile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
if (__pyx_t_1) {
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L14;
+ goto __pyx_L17;
}
- __pyx_L14:;
+ __pyx_L17:;
- /* "pysam/csamtools.pyx":656
+ /* "csamtools.pyx":656
* # close a previously opened file
* if self.samfile != NULL: self.close()
* self.samfile = NULL # <<<<<<<<<<<<<<
*
* cdef bam_header_t * header_to_write
*/
- __pyx_v_self->samfile = NULL;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
- /* "pysam/csamtools.pyx":659
+ /* "csamtools.pyx":659
*
* cdef bam_header_t * header_to_write
* header_to_write = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_header_to_write = NULL;
- /* "pysam/csamtools.pyx":661
+ /* "csamtools.pyx":661
* header_to_write = NULL
*
* if self._filename != NULL: free(self._filename ) # <<<<<<<<<<<<<<
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii')
*/
- __pyx_t_1 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_1) {
- free(__pyx_v_self->_filename);
- goto __pyx_L15;
+ free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
+ goto __pyx_L18;
}
- __pyx_L15:;
+ __pyx_L18:;
- /* "pysam/csamtools.pyx":662
+ /* "csamtools.pyx":662
*
* if self._filename != NULL: free(self._filename )
* filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<<
* cdef bytes bmode = mode.encode('ascii')
* #cdef char* cfilename
*/
- __pyx_t_8 = ((PyObject *)__pyx_f_5pysam_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_filename);
__pyx_v_filename = __pyx_t_8;
__pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":663
+ /* "csamtools.pyx":663
* if self._filename != NULL: free(self._filename )
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<<
__pyx_v_bmode = ((PyObject*)__pyx_t_5);
__pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":666
+ /* "csamtools.pyx":666
* #cdef char* cfilename
* #cfilename = filename.encode(_FILENAME_ENCODING)
* self._filename = strdup(filename) # <<<<<<<<<<<<<<
*
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_filename = strdup(__pyx_t_12);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = strdup(__pyx_t_12);
- /* "pysam/csamtools.pyx":667
+ /* "csamtools.pyx":667
* #cfilename = filename.encode(_FILENAME_ENCODING)
* self._filename = strdup(filename)
* self.isstream = strcmp( filename, "-" ) == 0 # <<<<<<<<<<<<<<
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
- /* "pysam/csamtools.pyx":669
+ /* "csamtools.pyx":669
* self.isstream = strcmp( filename, "-" ) == 0
*
* self.isbam = len(mode) > 1 and mode[1] == 'b' # <<<<<<<<<<<<<<
* self.isremote = strncmp(filename,"http:",5) == 0 or \
*/
__pyx_t_13 = PyObject_Length(__pyx_v_mode); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyBool_FromLong((__pyx_t_13 > 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__pyx_t_13 > 1);
if (__pyx_t_1) {
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__b), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_n_s__b), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_8 = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_11 = __pyx_t_1;
}
- __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_8); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_v_self->isbam = __pyx_t_9;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = __pyx_t_11;
- /* "pysam/csamtools.pyx":671
+ /* "csamtools.pyx":671
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*
* self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
*
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = (strncmp(__pyx_t_12, __pyx_k_27, 5) == 0);
- if (!__pyx_t_1) {
+ __pyx_t_11 = (strncmp(__pyx_t_12, __pyx_k_27, 5) == 0);
+ if (!__pyx_t_11) {
- /* "pysam/csamtools.pyx":672
+ /* "csamtools.pyx":672
*
* self.isremote = strncmp(filename,"http:",5) == 0 or \
* strncmp(filename,"ftp:",4) == 0 # <<<<<<<<<<<<<<
* cdef char * ctext
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = (strncmp(__pyx_t_12, __pyx_k_28, 4) == 0);
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_1 = (strncmp(__pyx_t_12, __pyx_k_28, 4) == 0);
+ __pyx_t_10 = __pyx_t_1;
} else {
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_10 = __pyx_t_11;
}
- /* "pysam/csamtools.pyx":671
+ /* "csamtools.pyx":671
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*
* self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
* strncmp(filename,"ftp:",4) == 0
*
*/
- __pyx_v_self->isremote = __pyx_t_11;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote = __pyx_t_10;
- /* "pysam/csamtools.pyx":675
+ /* "csamtools.pyx":675
*
* cdef char * ctext
* ctext = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_ctext = NULL;
- /* "pysam/csamtools.pyx":677
+ /* "csamtools.pyx":677
* ctext = NULL
*
* if mode[0] == 'w': # <<<<<<<<<<<<<<
* # open file for writing
*
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_n_s__w), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_11) {
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":681
+ /* "csamtools.pyx":681
*
* # header structure (used for writing)
* if template: # <<<<<<<<<<<<<<
* # copy header from another file
* header_to_write = template.samfile.header
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_11) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":683
+ /* "csamtools.pyx":683
* if template:
* # copy header from another file
* header_to_write = template.samfile.header # <<<<<<<<<<<<<<
*
* elif header:
*/
- __pyx_t_14 = __pyx_v_template->samfile->header;
- __pyx_v_header_to_write = __pyx_t_14;
- goto __pyx_L17;
+ __pyx_v_header_to_write = __pyx_v_template->samfile->header;
+ goto __pyx_L20;
}
- /* "pysam/csamtools.pyx":685
+ /* "csamtools.pyx":685
* header_to_write = template.samfile.header
*
* elif header: # <<<<<<<<<<<<<<
* header_to_write = self._buildHeader( header )
*
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_11) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":686
+ /* "csamtools.pyx":686
*
* elif header:
* header_to_write = self._buildHeader( header ) # <<<<<<<<<<<<<<
*
* else:
*/
- __pyx_v_header_to_write = ((struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->_buildHeader(__pyx_v_self, __pyx_v_header);
- goto __pyx_L17;
+ __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->_buildHeader(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_header);
+ goto __pyx_L20;
}
/*else*/ {
- /* "pysam/csamtools.pyx":690
+ /* "csamtools.pyx":690
* else:
* # build header from a target names and lengths
* assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" # <<<<<<<<<<<<<<
*
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_11) {
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_t_11;
} else {
- __pyx_t_10 = __pyx_t_11;
+ __pyx_t_1 = __pyx_t_10;
}
- if (unlikely(!__pyx_t_10)) {
+ if (unlikely(!__pyx_t_1)) {
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_29));
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":691
+ /* "csamtools.pyx":691
* # build header from a target names and lengths
* assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"
* assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" # <<<<<<<<<<<<<<
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
__pyx_t_13 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_15 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!(__pyx_t_13 == __pyx_t_15))) {
+ __pyx_t_14 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!(__pyx_t_13 == __pyx_t_14))) {
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_30));
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":694
+ /* "csamtools.pyx":694
*
* # allocate and fill header
* referencenames = [ _force_bytes(ref) for ref in referencenames ] # <<<<<<<<<<<<<<
* header_to_write.n_targets = len(referencenames)
*/
__pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
- __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
- __pyx_t_16 = NULL;
+ __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0;
+ __pyx_t_15 = NULL;
} else {
- __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_16 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
+ } else if (PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
} else {
- __pyx_t_7 = __pyx_t_16(__pyx_t_8);
+ __pyx_t_7 = __pyx_t_15(__pyx_t_8);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
__Pyx_XDECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_7;
__pyx_t_7 = 0;
- __pyx_t_7 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = ((PyObject *)__pyx_t_5);
- __Pyx_INCREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_5));
__Pyx_DECREF(__pyx_v_referencenames);
- __pyx_v_referencenames = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_referencenames = ((PyObject *)__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":695
+ /* "csamtools.pyx":695
* # allocate and fill header
* referencenames = [ _force_bytes(ref) for ref in referencenames ]
* header_to_write = bam_header_init() # <<<<<<<<<<<<<<
*/
__pyx_v_header_to_write = bam_header_init();
- /* "pysam/csamtools.pyx":696
+ /* "csamtools.pyx":696
* referencenames = [ _force_bytes(ref) for ref in referencenames ]
* header_to_write = bam_header_init()
* header_to_write.n_targets = len(referencenames) # <<<<<<<<<<<<<<
* n = 0
* for x in referencenames: n += len(x) + 1
*/
- __pyx_t_15 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->n_targets = __pyx_t_15;
+ __pyx_t_14 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->n_targets = __pyx_t_14;
- /* "pysam/csamtools.pyx":697
+ /* "csamtools.pyx":697
* header_to_write = bam_header_init()
* header_to_write.n_targets = len(referencenames)
* n = 0 # <<<<<<<<<<<<<<
__Pyx_INCREF(__pyx_int_0);
__pyx_v_n = __pyx_int_0;
- /* "pysam/csamtools.pyx":698
+ /* "csamtools.pyx":698
* header_to_write.n_targets = len(referencenames)
* n = 0
* for x in referencenames: n += len(x) + 1 # <<<<<<<<<<<<<<
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
*/
if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
- __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
- __pyx_t_16 = NULL;
+ __pyx_t_5 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0;
+ __pyx_t_15 = NULL;
} else {
- __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_16 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_14 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_15 = Py_TYPE(__pyx_t_5)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_5 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_5); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_5 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_5); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_5 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (PyList_CheckExact(__pyx_t_5)) {
+ if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
+ } else if (PyTuple_CheckExact(__pyx_t_5)) {
+ if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
} else {
- __pyx_t_5 = __pyx_t_16(__pyx_t_8);
- if (unlikely(!__pyx_t_5)) {
+ __pyx_t_8 = __pyx_t_15(__pyx_t_5);
+ if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(__pyx_t_8);
}
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
__pyx_t_13 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_v_n);
__pyx_v_n = __pyx_t_7;
__pyx_t_7 = 0;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":699
+ /* "csamtools.pyx":699
* n = 0
* for x in referencenames: n += len(x) + 1
* header_to_write.target_name = <char**>calloc(n, sizeof(char*)) # <<<<<<<<<<<<<<
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets:
*/
- __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_17, (sizeof(char *))));
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_16, (sizeof(char *))));
- /* "pysam/csamtools.pyx":700
+ /* "csamtools.pyx":700
* for x in referencenames: n += len(x) + 1
* header_to_write.target_name = <char**>calloc(n, sizeof(char*))
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t)) # <<<<<<<<<<<<<<
* for x from 0 <= x < header_to_write.n_targets:
* header_to_write.target_len[x] = referencelengths[x]
*/
- __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_17, (sizeof(uint32_t))));
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_16, (sizeof(uint32_t))));
- /* "pysam/csamtools.pyx":701
+ /* "csamtools.pyx":701
* header_to_write.target_name = <char**>calloc(n, sizeof(char*))
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x]
*/
- __pyx_t_18 = __pyx_v_header_to_write->n_targets;
- for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19++) {
- __pyx_t_8 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_17 = __pyx_v_header_to_write->n_targets;
+ for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18++) {
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":702
+ /* "csamtools.pyx":702
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets:
* header_to_write.target_len[x] = referencelengths[x] # <<<<<<<<<<<<<<
* name = referencenames[x]
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_20 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_20 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_15 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_15 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_header_to_write->target_len[__pyx_t_15]) = __pyx_t_20;
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_19 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_19 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_14 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_14 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_header_to_write->target_len[__pyx_t_14]) = __pyx_t_19;
- /* "pysam/csamtools.pyx":703
+ /* "csamtools.pyx":703
* for x from 0 <= x < header_to_write.n_targets:
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x] # <<<<<<<<<<<<<<
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
* strncpy( header_to_write.target_name[x], name, len(name) )
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_v_name);
- __pyx_v_name = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_name = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":704
+ /* "csamtools.pyx":704
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x]
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char)) # <<<<<<<<<<<<<<
* strncpy( header_to_write.target_name[x], name, len(name) )
*
*/
- __pyx_t_15 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_13 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_header_to_write->target_name[__pyx_t_13]) = ((char *)calloc((__pyx_t_15 + 1), (sizeof(char))));
+ (__pyx_v_header_to_write->target_name[__pyx_t_13]) = ((char *)calloc((__pyx_t_14 + 1), (sizeof(char))));
- /* "pysam/csamtools.pyx":705
+ /* "csamtools.pyx":705
* name = referencenames[x]
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
* strncpy( header_to_write.target_name[x], name, len(name) ) # <<<<<<<<<<<<<<
*
* # Optionally, if there is no text, add a SAM compatible header to output
*/
- __pyx_t_15 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_15 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_14 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(__pyx_v_name); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy((__pyx_v_header_to_write->target_name[__pyx_t_15]), __pyx_t_12, __pyx_t_13);
- __pyx_t_19 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_19 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy((__pyx_v_header_to_write->target_name[__pyx_t_14]), __pyx_t_12, __pyx_t_13);
+ __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "pysam/csamtools.pyx":701
+ /* "csamtools.pyx":701
* header_to_write.target_name = <char**>calloc(n, sizeof(char*))
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x]
*/
- __pyx_t_8 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":709
+ /* "csamtools.pyx":709
* # Optionally, if there is no text, add a SAM compatible header to output
* # file.
* if text is None and add_sq_text: # <<<<<<<<<<<<<<
* text = []
* for x from 0 <= x < header_to_write.n_targets:
*/
- __pyx_t_10 = (__pyx_v_text == Py_None);
- if (__pyx_t_10) {
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_add_sq_text); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __pyx_t_11;
+ __pyx_t_1 = (__pyx_v_text == Py_None);
+ if (__pyx_t_1) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_add_sq_text); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_1 = __pyx_t_10;
+ __pyx_t_11 = __pyx_t_1;
}
- if (__pyx_t_1) {
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":710
+ /* "csamtools.pyx":710
* # file.
* if text is None and add_sq_text:
* text = [] # <<<<<<<<<<<<<<
* for x from 0 <= x < header_to_write.n_targets:
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
__Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = ((PyObject *)__pyx_t_8);
- __pyx_t_8 = 0;
+ __pyx_v_text = ((PyObject *)__pyx_t_5);
+ __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":711
+ /* "csamtools.pyx":711
* if text is None and add_sq_text:
* text = []
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
* text = ''.join(text)
*/
- __pyx_t_18 = __pyx_v_header_to_write->n_targets;
- for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19++) {
- __pyx_t_8 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_17 = __pyx_v_header_to_write->n_targets;
+ for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18++) {
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":712
+ /* "csamtools.pyx":712
* text = []
* for x from 0 <= x < header_to_write.n_targets:
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) ) # <<<<<<<<<<<<<<
* text = ''.join(text)
*
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_7);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_8 = 0;
+ __pyx_t_5 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_31), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_31), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_text, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = __Pyx_PyObject_Append(__pyx_v_text, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_19 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_19 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "pysam/csamtools.pyx":711
+ /* "csamtools.pyx":711
* if text is None and add_sq_text:
* text = []
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
* text = ''.join(text)
*/
- __pyx_t_5 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":713
+ /* "csamtools.pyx":713
* for x from 0 <= x < header_to_write.n_targets:
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
* text = ''.join(text) # <<<<<<<<<<<<<<
*
* if text != None:
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_text);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_text);
__Pyx_GIVEREF(__pyx_v_text);
- __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = __pyx_t_8;
- __pyx_t_8 = 0;
- goto __pyx_L24;
+ __pyx_v_text = __pyx_t_5;
+ __pyx_t_5 = 0;
+ goto __pyx_L27;
}
- __pyx_L24:;
+ __pyx_L27:;
- /* "pysam/csamtools.pyx":715
+ /* "csamtools.pyx":715
* text = ''.join(text)
*
* if text != None: # <<<<<<<<<<<<<<
* # copy without \0
* text = _force_bytes(text)
*/
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_text, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_1) {
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_text, Py_None, Py_NE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":717
+ /* "csamtools.pyx":717
* if text != None:
* # copy without \0
* text = _force_bytes(text) # <<<<<<<<<<<<<<
* ctext = text
* header_to_write.l_text = strlen(ctext)
*/
- __pyx_t_8 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_text)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_text)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_text = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":718
+ /* "csamtools.pyx":718
* # copy without \0
* text = _force_bytes(text)
* ctext = text # <<<<<<<<<<<<<<
__pyx_t_12 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_ctext = __pyx_t_12;
- /* "pysam/csamtools.pyx":719
+ /* "csamtools.pyx":719
* text = _force_bytes(text)
* ctext = text
* header_to_write.l_text = strlen(ctext) # <<<<<<<<<<<<<<
*/
__pyx_v_header_to_write->l_text = strlen(__pyx_v_ctext);
- /* "pysam/csamtools.pyx":720
+ /* "csamtools.pyx":720
* ctext = text
* header_to_write.l_text = strlen(ctext)
* header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) ) # <<<<<<<<<<<<<<
*/
__pyx_v_header_to_write->text = ((char *)calloc(strlen(__pyx_v_ctext), (sizeof(char))));
- /* "pysam/csamtools.pyx":721
+ /* "csamtools.pyx":721
* header_to_write.l_text = strlen(ctext)
* header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
* memcpy( header_to_write.text, ctext, strlen(ctext) ) # <<<<<<<<<<<<<<
* header_to_write.hash = NULL
*/
memcpy(__pyx_v_header_to_write->text, __pyx_v_ctext, strlen(__pyx_v_ctext));
- goto __pyx_L27;
+ goto __pyx_L30;
}
- __pyx_L27:;
+ __pyx_L30:;
- /* "pysam/csamtools.pyx":723
+ /* "csamtools.pyx":723
* memcpy( header_to_write.text, ctext, strlen(ctext) )
*
* header_to_write.hash = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_header_to_write->hash = NULL;
- /* "pysam/csamtools.pyx":724
+ /* "csamtools.pyx":724
*
* header_to_write.hash = NULL
* header_to_write.rg2lib = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_header_to_write->rg2lib = NULL;
}
- __pyx_L17:;
+ __pyx_L20:;
- /* "pysam/csamtools.pyx":728
+ /* "csamtools.pyx":728
* # open file. Header gets written to file at the same time for bam files
* # and sam files (in the latter case, the mode needs to be wh)
* store = StderrStore() # <<<<<<<<<<<<<<
* self.samfile = samopen( filename, bmode, header_to_write )
* store.release()
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_store = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":729
+ /* "csamtools.pyx":729
* # and sam files (in the latter case, the mode needs to be wh)
* store = StderrStore()
* self.samfile = samopen( filename, bmode, header_to_write ) # <<<<<<<<<<<<<<
* store.release()
*
*/
- __pyx_t_21 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_21 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->samfile = samopen(__pyx_t_21, __pyx_t_12, __pyx_v_header_to_write);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write);
- /* "pysam/csamtools.pyx":730
+ /* "csamtools.pyx":730
* store = StderrStore()
* self.samfile = samopen( filename, bmode, header_to_write )
* store.release() # <<<<<<<<<<<<<<
*/
__pyx_t_7 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":733
+ /* "csamtools.pyx":733
*
* # bam_header_destroy takes care of cleaning up of all the members
* if not template and header_to_write != NULL: # <<<<<<<<<<<<<<
* bam_header_destroy( header_to_write )
*
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = (!__pyx_t_1);
- if (__pyx_t_10) {
- __pyx_t_1 = (__pyx_v_header_to_write != NULL);
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (!__pyx_t_11);
+ if (__pyx_t_1) {
+ __pyx_t_11 = (__pyx_v_header_to_write != NULL);
+ __pyx_t_10 = __pyx_t_11;
} else {
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_10 = __pyx_t_1;
}
- if (__pyx_t_11) {
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":734
+ /* "csamtools.pyx":734
* # bam_header_destroy takes care of cleaning up of all the members
* if not template and header_to_write != NULL:
* bam_header_destroy( header_to_write ) # <<<<<<<<<<<<<<
* elif mode[0] == "r":
*/
bam_header_destroy(__pyx_v_header_to_write);
- goto __pyx_L28;
+ goto __pyx_L31;
}
- __pyx_L28:;
- goto __pyx_L16;
+ __pyx_L31:;
+ goto __pyx_L19;
}
- /* "pysam/csamtools.pyx":736
+ /* "csamtools.pyx":736
* bam_header_destroy( header_to_write )
*
* elif mode[0] == "r": # <<<<<<<<<<<<<<
* # open file for reading
* if strncmp( filename, "-", 1) != 0 and \
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_11) {
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":738
+ /* "csamtools.pyx":738
* elif mode[0] == "r":
* # open file for reading
* if strncmp( filename, "-", 1) != 0 and \ # <<<<<<<<<<<<<<
* not os.path.exists( filename ):
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = (strncmp(__pyx_t_12, __pyx_k_26, 1) != 0);
- if (__pyx_t_11) {
+ __pyx_t_10 = (strncmp(__pyx_t_12, __pyx_k_26, 1) != 0);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":739
+ /* "csamtools.pyx":739
* # open file for reading
* if strncmp( filename, "-", 1) != 0 and \
* not self.isremote and \ # <<<<<<<<<<<<<<
* not os.path.exists( filename ):
* raise IOError( "file `%s` not found" % filename)
*/
- __pyx_t_10 = (!__pyx_v_self->isremote);
- if (__pyx_t_10) {
+ __pyx_t_1 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":740
+ /* "csamtools.pyx":740
* if strncmp( filename, "-", 1) != 0 and \
* not self.isremote and \
* not os.path.exists( filename ): # <<<<<<<<<<<<<<
* raise IOError( "file `%s` not found" % filename)
*
*/
- __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__path); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__exists); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_22 = (!__pyx_t_1);
- __pyx_t_1 = __pyx_t_22;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_21 = (!__pyx_t_11);
+ __pyx_t_11 = __pyx_t_21;
} else {
- __pyx_t_1 = __pyx_t_10;
+ __pyx_t_11 = __pyx_t_1;
}
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_1 = __pyx_t_11;
} else {
- __pyx_t_10 = __pyx_t_11;
+ __pyx_t_1 = __pyx_t_10;
}
- if (__pyx_t_10) {
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":741
+ /* "csamtools.pyx":741
* not self.isremote and \
* not os.path.exists( filename ):
* raise IOError( "file `%s` not found" % filename) # <<<<<<<<<<<<<<
*
* # try to detect errors
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L29;
+ goto __pyx_L32;
}
- __pyx_L29:;
+ __pyx_L32:;
- /* "pysam/csamtools.pyx":744
+ /* "csamtools.pyx":744
*
* # try to detect errors
* self.samfile = samopen( filename, bmode, NULL ) # <<<<<<<<<<<<<<
* if self.samfile == NULL:
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
*/
- __pyx_t_21 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_21 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->samfile = samopen(__pyx_t_21, __pyx_t_12, NULL);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL);
- /* "pysam/csamtools.pyx":745
+ /* "csamtools.pyx":745
* # try to detect errors
* self.samfile = samopen( filename, bmode, NULL )
* if self.samfile == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
*
*/
- __pyx_t_10 = (__pyx_v_self->samfile == NULL);
- if (__pyx_t_10) {
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":746
+ /* "csamtools.pyx":746
* self.samfile = samopen( filename, bmode, NULL )
* if self.samfile == NULL:
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
*
* # bam files require a valid header
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L30;
+ goto __pyx_L33;
}
- __pyx_L30:;
+ __pyx_L33:;
- /* "pysam/csamtools.pyx":749
+ /* "csamtools.pyx":749
*
* # bam files require a valid header
* if self.isbam: # <<<<<<<<<<<<<<
* if self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
- /* "pysam/csamtools.pyx":750
+ /* "csamtools.pyx":750
* # bam files require a valid header
* if self.isbam:
* if self.samfile.header == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
* else:
*/
- __pyx_t_10 = (__pyx_v_self->samfile->header == NULL);
- if (__pyx_t_10) {
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":751
+ /* "csamtools.pyx":751
* if self.isbam:
* if self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) # <<<<<<<<<<<<<<
* else:
* # in sam files it is optional (samfile full of unmapped reads)
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ goto __pyx_L35;
}
- __pyx_L32:;
- goto __pyx_L31;
+ __pyx_L35:;
+ goto __pyx_L34;
}
/*else*/ {
- /* "pysam/csamtools.pyx":754
+ /* "csamtools.pyx":754
* else:
* # in sam files it is optional (samfile full of unmapped reads)
* if check_header and self.samfile.header == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode )
*
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_10) {
- __pyx_t_11 = (__pyx_v_self->samfile->header == NULL);
- __pyx_t_1 = __pyx_t_11;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_1 = __pyx_t_10;
+ __pyx_t_11 = __pyx_t_1;
}
- if (__pyx_t_1) {
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":755
+ /* "csamtools.pyx":755
* # in sam files it is optional (samfile full of unmapped reads)
* if check_header and self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode ) # <<<<<<<<<<<<<<
*
* # disabled for autodetection to work
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L33;
+ goto __pyx_L36;
}
- __pyx_L33:;
+ __pyx_L36:;
}
- __pyx_L31:;
+ __pyx_L34:;
- /* "pysam/csamtools.pyx":759
+ /* "csamtools.pyx":759
* # disabled for autodetection to work
* # needs to be disabled so that reading from sam-files without headers works
* if check_sq and self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
*
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- __pyx_t_10 = (__pyx_v_self->samfile->header->n_targets == 0);
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_11) {
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
+ __pyx_t_10 = __pyx_t_1;
} else {
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_10 = __pyx_t_11;
}
- if (__pyx_t_11) {
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":760
+ /* "csamtools.pyx":760
* # needs to be disabled so that reading from sam-files without headers works
* if check_sq and self.samfile.header.n_targets == 0:
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
*
* if self.samfile == NULL:
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L34;
+ goto __pyx_L37;
}
- __pyx_L34:;
- goto __pyx_L16;
+ __pyx_L37:;
+ goto __pyx_L19;
}
- __pyx_L16:;
+ __pyx_L19:;
- /* "pysam/csamtools.pyx":762
+ /* "csamtools.pyx":762
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
*
* if self.samfile == NULL: # <<<<<<<<<<<<<<
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_11 = (__pyx_v_self->samfile == NULL);
- if (__pyx_t_11) {
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":763
+ /* "csamtools.pyx":763
*
* if self.samfile == NULL:
* raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
*
* # check for index and open if present
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L35;
+ goto __pyx_L38;
}
- __pyx_L35:;
+ __pyx_L38:;
- /* "pysam/csamtools.pyx":766
+ /* "csamtools.pyx":766
*
* # check for index and open if present
* if mode[0] == "r" and self.isbam: # <<<<<<<<<<<<<<
*
* if not self.isremote:
*/
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_11) {
- __pyx_t_1 = __pyx_v_self->isbam;
+ if (__pyx_t_10) {
+ __pyx_t_11 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam;
} else {
- __pyx_t_1 = __pyx_t_11;
+ __pyx_t_11 = __pyx_t_10;
}
- if (__pyx_t_1) {
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":768
+ /* "csamtools.pyx":768
* if mode[0] == "r" and self.isbam:
*
* if not self.isremote: # <<<<<<<<<<<<<<
* if not os.path.exists(filename + b".bai"):
* self.index = NULL
*/
- __pyx_t_1 = (!__pyx_v_self->isremote);
- if (__pyx_t_1) {
+ __pyx_t_11 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":769
+ /* "csamtools.pyx":769
*
* if not self.isremote:
* if not os.path.exists(filename + b".bai"): # <<<<<<<<<<<<<<
*/
__pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__path); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__exists); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_11 = (!__pyx_t_1);
- if (__pyx_t_11) {
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_10 = (!__pyx_t_11);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":770
+ /* "csamtools.pyx":770
* if not self.isremote:
* if not os.path.exists(filename + b".bai"):
* self.index = NULL # <<<<<<<<<<<<<<
* else:
* # returns NULL if there is no index or index could not be opened
*/
- __pyx_v_self->index = NULL;
- goto __pyx_L38;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = NULL;
+ goto __pyx_L41;
}
/*else*/ {
- /* "pysam/csamtools.pyx":773
+ /* "csamtools.pyx":773
* else:
* # returns NULL if there is no index or index could not be opened
* self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
* raise IOError("error while opening index `%s` " % filename )
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->index = bam_index_load(__pyx_t_12);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12);
- /* "pysam/csamtools.pyx":774
+ /* "csamtools.pyx":774
* # returns NULL if there is no index or index could not be opened
* self.index = bam_index_load(filename)
* if self.index == NULL: # <<<<<<<<<<<<<<
* raise IOError("error while opening index `%s` " % filename )
* else:
*/
- __pyx_t_11 = (__pyx_v_self->index == NULL);
- if (__pyx_t_11) {
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":775
+ /* "csamtools.pyx":775
* self.index = bam_index_load(filename)
* if self.index == NULL:
* raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
* else:
* self.index = bam_index_load(filename)
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L39;
+ goto __pyx_L42;
}
- __pyx_L39:;
+ __pyx_L42:;
}
- __pyx_L38:;
- goto __pyx_L37;
+ __pyx_L41:;
+ goto __pyx_L40;
}
/*else*/ {
- /* "pysam/csamtools.pyx":777
+ /* "csamtools.pyx":777
* raise IOError("error while opening index `%s` " % filename )
* else:
* self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
* raise IOError("error while opening index `%s` " % filename )
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->index = bam_index_load(__pyx_t_12);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12);
- /* "pysam/csamtools.pyx":778
+ /* "csamtools.pyx":778
* else:
* self.index = bam_index_load(filename)
* if self.index == NULL: # <<<<<<<<<<<<<<
* raise IOError("error while opening index `%s` " % filename )
*
*/
- __pyx_t_11 = (__pyx_v_self->index == NULL);
- if (__pyx_t_11) {
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":779
+ /* "csamtools.pyx":779
* self.index = bam_index_load(filename)
* if self.index == NULL:
* raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
*
* if not self.isstream:
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L40;
+ goto __pyx_L43;
}
- __pyx_L40:;
+ __pyx_L43:;
}
- __pyx_L37:;
+ __pyx_L40:;
- /* "pysam/csamtools.pyx":781
+ /* "csamtools.pyx":781
* raise IOError("error while opening index `%s` " % filename )
*
* if not self.isstream: # <<<<<<<<<<<<<<
* self.start_offset = bam_tell( self.samfile.x.bam )
*
*/
- __pyx_t_11 = (!__pyx_v_self->isstream);
- if (__pyx_t_11) {
+ __pyx_t_10 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":782
+ /* "csamtools.pyx":782
*
* if not self.isstream:
* self.start_offset = bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
*
* def gettid( self, reference ):
*/
- __pyx_v_self->start_offset = bam_tell(__pyx_v_self->samfile->x.bam);
- goto __pyx_L41;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset = bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam);
+ goto __pyx_L44;
}
- __pyx_L41:;
- goto __pyx_L36;
+ __pyx_L44:;
+ goto __pyx_L39;
}
- __pyx_L36:;
+ __pyx_L39:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("pysam.csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_msg);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_8gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("gettid (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_8gettid(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_reference));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":784
+/* "csamtools.pyx":784
* self.start_offset = bam_tell( self.samfile.x.bam )
*
* def gettid( self, reference ): # <<<<<<<<<<<<<<
* convert :term:`reference` name into numerical :term:`tid`
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8gettid(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_4gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("gettid", 0);
+ __Pyx_RefNannySetupContext("gettid");
__Pyx_TraceCall("gettid", __pyx_f[0], 784);
__Pyx_INCREF(__pyx_v_reference);
- /* "pysam/csamtools.pyx":790
+ /* "csamtools.pyx":790
* returns -1 if reference is not known.
* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":791
+ /* "csamtools.pyx":791
* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* reference = _force_bytes(reference) # <<<<<<<<<<<<<<
* return pysam_reference2tid( self.samfile.header, reference )
*
*/
- __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_reference)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_reference)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_reference);
__pyx_v_reference = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":792
+ /* "csamtools.pyx":792
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference ) # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(__pyx_v_self->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.gettid", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.gettid", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_reference);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_10getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("getrname (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_10getrname(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":794
+/* "csamtools.pyx":794
* return pysam_reference2tid( self.samfile.header, reference )
*
* def getrname( self, tid ): # <<<<<<<<<<<<<<
* convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_5getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getrname", 0);
+ __Pyx_RefNannySetupContext("getrname");
__Pyx_TraceCall("getrname", __pyx_f[0], 794);
- /* "pysam/csamtools.pyx":797
+ /* "csamtools.pyx":797
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":798
+ /* "csamtools.pyx":798
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
* return _charptr_to_str(self.samfile.header.target_name[tid])
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_int_0, __pyx_v_tid, Py_LE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_int_0, __pyx_v_tid, Py_LE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
if (__Pyx_PyObject_IsTrue(__pyx_t_2)) {
__Pyx_DECREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":799
+ /* "csamtools.pyx":799
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
* return _charptr_to_str(self.samfile.header.target_name[tid])
*
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_tid);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_tid);
__Pyx_GIVEREF(__pyx_v_tid);
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":800
+ /* "csamtools.pyx":800
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
* return _charptr_to_str(self.samfile.header.target_name[tid]) # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_tid); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __pyx_f_5pysam_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":802
+/* "csamtools.pyx":802
* return _charptr_to_str(self.samfile.header.target_name[tid])
*
* cdef char * _getrname( self, int tid ): # TODO unused # <<<<<<<<<<<<<<
* convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static char *__pyx_f_5pysam_9csamtools_7Samfile__getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, int __pyx_v_tid) {
+static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, int __pyx_v_tid) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_getrname", 0);
+ __Pyx_RefNannySetupContext("_getrname");
__Pyx_TraceCall("_getrname", __pyx_f[0], 802);
- /* "pysam/csamtools.pyx":805
+ /* "csamtools.pyx":805
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":806
+ /* "csamtools.pyx":806
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":807
+ /* "csamtools.pyx":807
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
__pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
}
__pyx_L4:;
- /* "pysam/csamtools.pyx":808
+ /* "csamtools.pyx":808
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
* return self.samfile.header.target_name[tid] # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_WriteUnraisable("pysam.csamtools.Samfile._getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.Samfile._getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_12_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":810
+ * return self.samfile.header.target_name[tid]
+ *
+ * def _parseRegion( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_6_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ PY_LONG_LONG __pyx_v_rstart;
+ PY_LONG_LONG __pyx_v_rend;
+ PyObject *__pyx_v_parts = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_parseRegion (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PY_LONG_LONG __pyx_t_6;
+ int __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_parseRegion");
+ __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[4] = {0,0,0,0};
- /* "pysam/csamtools.pyx":811
+ /* "csamtools.pyx":811
*
* def _parseRegion( self,
* reference = None, # <<<<<<<<<<<<<<
*/
values[0] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":812
+ /* "csamtools.pyx":812
* def _parseRegion( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":813
+ /* "csamtools.pyx":813
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
*/
values[2] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":814
+ /* "csamtools.pyx":814
* start = None,
* end = None,
* region = None ): # <<<<<<<<<<<<<<
values[3] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("_parseRegion", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":810
- * return self.samfile.header.target_name[tid]
- *
- * def _parseRegion( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
- int __pyx_v_rtid;
- PY_LONG_LONG __pyx_v_rstart;
- PY_LONG_LONG __pyx_v_rend;
- PyObject *__pyx_v_parts = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PY_LONG_LONG __pyx_t_6;
- int __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- Py_ssize_t __pyx_t_12;
- int __pyx_t_13;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_parseRegion", 0);
- __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810);
__Pyx_INCREF(__pyx_v_reference);
__Pyx_INCREF(__pyx_v_region);
- /* "pysam/csamtools.pyx":833
+ /* "csamtools.pyx":833
* cdef long long rend
*
* rtid = -1 # <<<<<<<<<<<<<<
*/
__pyx_v_rtid = -1;
- /* "pysam/csamtools.pyx":834
+ /* "csamtools.pyx":834
*
* rtid = -1
* rstart = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_rstart = 0;
- /* "pysam/csamtools.pyx":835
+ /* "csamtools.pyx":835
* rtid = -1
* rstart = 0
* rend = max_pos # <<<<<<<<<<<<<<
* if start != None:
* try:
*/
- __pyx_v_rend = __pyx_v_5pysam_9csamtools_max_pos;
+ __pyx_v_rend = __pyx_v_9csamtools_max_pos;
- /* "pysam/csamtools.pyx":836
+ /* "csamtools.pyx":836
* rstart = 0
* rend = max_pos
* if start != None: # <<<<<<<<<<<<<<
* try:
* rstart = start
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":837
+ /* "csamtools.pyx":837
* rend = max_pos
* if start != None:
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_5);
/*try:*/ {
- /* "pysam/csamtools.pyx":838
+ /* "csamtools.pyx":838
* if start != None:
* try:
* rstart = start # <<<<<<<<<<<<<<
* except OverflowError:
* raise ValueError( 'start out of range (%i)' % start )
*/
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__pyx_v_rstart = __pyx_t_6;
}
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- goto __pyx_L11_try_end;
- __pyx_L4_error:;
+ goto __pyx_L14_try_end;
+ __pyx_L7_error:;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":839
+ /* "csamtools.pyx":839
* try:
* rstart = start
* except OverflowError: # <<<<<<<<<<<<<<
*/
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
if (__pyx_t_7) {
- __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_9);
- /* "pysam/csamtools.pyx":840
+ /* "csamtools.pyx":840
* rstart = start
* except OverflowError:
* raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
*
* if end != None:
*/
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_Raise(__pyx_t_10, 0, 0, 0);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L5_exception_handled;
+ goto __pyx_L8_exception_handled;
}
- __pyx_L6_except_error:;
+ __pyx_L9_except_error:;
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
goto __pyx_L1_error;
- __pyx_L5_exception_handled:;
+ __pyx_L8_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
- __pyx_L11_try_end:;
+ __pyx_L14_try_end:;
}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":842
+ /* "csamtools.pyx":842
* raise ValueError( 'start out of range (%i)' % start )
*
* if end != None: # <<<<<<<<<<<<<<
* try:
* rend = end
*/
- __pyx_t_9 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":843
+ /* "csamtools.pyx":843
*
* if end != None:
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_3);
/*try:*/ {
- /* "pysam/csamtools.pyx":844
+ /* "csamtools.pyx":844
* if end != None:
* try:
* rend = end # <<<<<<<<<<<<<<
* except OverflowError:
* raise ValueError( 'end out of range (%i)' % end )
*/
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L18_error;}
__pyx_v_rend = __pyx_t_6;
}
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L22_try_end;
- __pyx_L15_error:;
+ goto __pyx_L25_try_end;
+ __pyx_L18_error:;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":845
+ /* "csamtools.pyx":845
* try:
* rend = end
* except OverflowError: # <<<<<<<<<<<<<<
*/
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
if (__pyx_t_7) {
- __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":846
+ /* "csamtools.pyx":846
* rend = end
* except OverflowError:
* raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
*
* if region:
*/
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_Raise(__pyx_t_10, 0, 0, 0);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L16_exception_handled;
+ goto __pyx_L19_exception_handled;
}
- __pyx_L17_except_error:;
+ __pyx_L20_except_error:;
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
goto __pyx_L1_error;
- __pyx_L16_exception_handled:;
+ __pyx_L19_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
- __pyx_L22_try_end:;
+ __pyx_L25_try_end:;
}
- goto __pyx_L14;
+ goto __pyx_L17;
}
- __pyx_L14:;
+ __pyx_L17:;
- /* "pysam/csamtools.pyx":848
+ /* "csamtools.pyx":848
* raise ValueError( 'end out of range (%i)' % end )
*
* if region: # <<<<<<<<<<<<<<
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":849
+ /* "csamtools.pyx":849
*
* if region:
* region = _force_str(region) # <<<<<<<<<<<<<<
* parts = re.split( "[:-]", region )
* reference = parts[0]
*/
- __pyx_t_1 = __pyx_f_5pysam_9csamtools__force_str(__pyx_v_region); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools__force_str(__pyx_v_region); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":850
+ /* "csamtools.pyx":850
* if region:
* region = _force_str(region)
* parts = re.split( "[:-]", region ) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_43));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
__pyx_v_parts = __pyx_t_9;
__pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":851
+ /* "csamtools.pyx":851
* region = _force_str(region)
* parts = re.split( "[:-]", region )
* reference = parts[0] # <<<<<<<<<<<<<<
__pyx_v_reference = __pyx_t_9;
__pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":852
+ /* "csamtools.pyx":852
* parts = re.split( "[:-]", region )
* reference = parts[0]
* if len(parts) >= 2: rstart = int(parts[1]) - 1 # <<<<<<<<<<<<<<
__pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
__pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rstart = __pyx_t_6;
- goto __pyx_L26;
+ goto __pyx_L29;
}
- __pyx_L26:;
+ __pyx_L29:;
- /* "pysam/csamtools.pyx":853
+ /* "csamtools.pyx":853
* reference = parts[0]
* if len(parts) >= 2: rstart = int(parts[1]) - 1
* if len(parts) >= 3: rend = int(parts[2]) # <<<<<<<<<<<<<<
__pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rend = __pyx_t_6;
- goto __pyx_L27;
+ goto __pyx_L30;
}
- __pyx_L27:;
- goto __pyx_L25;
+ __pyx_L30:;
+ goto __pyx_L28;
}
- __pyx_L25:;
+ __pyx_L28:;
- /* "pysam/csamtools.pyx":855
+ /* "csamtools.pyx":855
* if len(parts) >= 3: rend = int(parts[2])
*
* if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
__Pyx_INCREF(((PyObject *)__pyx_k_tuple_44));
__pyx_r = ((PyObject *)__pyx_k_tuple_44);
goto __pyx_L0;
- goto __pyx_L28;
+ goto __pyx_L31;
}
- __pyx_L28:;
+ __pyx_L31:;
- /* "pysam/csamtools.pyx":857
+ /* "csamtools.pyx":857
* if not reference: return 0, 0, 0, 0
*
* rtid = self.gettid( reference ) # <<<<<<<<<<<<<<
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_rtid = __pyx_t_7;
- /* "pysam/csamtools.pyx":858
+ /* "csamtools.pyx":858
*
* rtid = self.gettid( reference )
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) # <<<<<<<<<<<<<<
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L29;
+ goto __pyx_L32;
}
- __pyx_L29:;
+ __pyx_L32:;
- /* "pysam/csamtools.pyx":859
+ /* "csamtools.pyx":859
* rtid = self.gettid( reference )
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) # <<<<<<<<<<<<<<
__pyx_t_9 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_9);
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L30;
+ goto __pyx_L33;
}
- __pyx_L30:;
+ __pyx_L33:;
- /* "pysam/csamtools.pyx":860
+ /* "csamtools.pyx":860
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
* if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) # <<<<<<<<<<<<<<
*/
__pyx_t_13 = (0 <= __pyx_v_rstart);
if (__pyx_t_13) {
- __pyx_t_13 = (__pyx_v_rstart < __pyx_v_5pysam_9csamtools_max_pos);
+ __pyx_t_13 = (__pyx_v_rstart < __pyx_v_9csamtools_max_pos);
}
__pyx_t_2 = (!__pyx_t_13);
if (__pyx_t_2) {
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L31;
+ goto __pyx_L34;
}
- __pyx_L31:;
+ __pyx_L34:;
- /* "pysam/csamtools.pyx":861
+ /* "csamtools.pyx":861
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
* if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
* if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend ) # <<<<<<<<<<<<<<
*/
__pyx_t_2 = (0 <= __pyx_v_rend);
if (__pyx_t_2) {
- __pyx_t_2 = (__pyx_v_rend <= __pyx_v_5pysam_9csamtools_max_pos);
+ __pyx_t_2 = (__pyx_v_rend <= __pyx_v_9csamtools_max_pos);
}
__pyx_t_13 = (!__pyx_t_2);
if (__pyx_t_13) {
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ goto __pyx_L35;
}
- __pyx_L32:;
+ __pyx_L35:;
- /* "pysam/csamtools.pyx":863
+ /* "csamtools.pyx":863
* if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
*
* return 1, rtid, rstart, rend # <<<<<<<<<<<<<<
__pyx_t_8 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
__Pyx_INCREF(__pyx_int_1);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_int_1);
__Pyx_GIVEREF(__pyx_int_1);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_parts);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_14reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("reset (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_14reset(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":865
+/* "csamtools.pyx":865
* return 1, rtid, rstart, rend
*
* def reset( self ): # <<<<<<<<<<<<<<
* return self.seek( self.start_offset, 0 )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_14reset(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_7reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_RefNannySetupContext("reset");
__Pyx_TraceCall("reset", __pyx_f[0], 865);
- /* "pysam/csamtools.pyx":867
+ /* "csamtools.pyx":867
* def reset( self ):
* '''reset file position to beginning of read section.'''
* return self.seek( self.start_offset, 0 ) # <<<<<<<<<<<<<<
* def seek( self, uint64_t offset, int where = 0):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_int_0);
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_16seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":869
+ * return self.seek( self.start_offset, 0 )
+ *
+ * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
+ * '''
+ * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_8seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
uint64_t __pyx_v_offset;
int __pyx_v_where;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("seek (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("seek");
+ __Pyx_TraceCall("seek", __pyx_f[0], 869);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_16seek(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_offset, __pyx_v_where);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":869
- * return self.seek( self.start_offset, 0 )
- *
- * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
- * '''
- * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
- */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_16seek(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("seek", 0);
- __Pyx_TraceCall("seek", __pyx_f[0], 869);
-
- /* "pysam/csamtools.pyx":874
+ /* "csamtools.pyx":874
* '''
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":875
+ /* "csamtools.pyx":875
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":876
+ /* "csamtools.pyx":876
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam: # <<<<<<<<<<<<<<
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":877
+ /* "csamtools.pyx":877
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":878
+ /* "csamtools.pyx":878
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
* if self.isstream: # <<<<<<<<<<<<<<
* raise OSError("seek no available in streams")
*
*/
- if (__pyx_v_self->isstream) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) {
- /* "pysam/csamtools.pyx":879
+ /* "csamtools.pyx":879
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
* raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L8;
}
- __pyx_L5:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":881
+ /* "csamtools.pyx":881
* raise OSError("seek no available in streams")
*
* return bam_seek( self.samfile.x.bam, offset, where ) # <<<<<<<<<<<<<<
* def tell( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(__pyx_v_self->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_18tell[] = "Samfile.tell(self)\n\n return current file position\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("tell (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_18tell(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":883
+/* "csamtools.pyx":883
* return bam_seek( self.samfile.x.bam, offset, where )
*
* def tell( self ): # <<<<<<<<<<<<<<
* return current file position
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_18tell(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_9tell[] = "Samfile.tell(self)\n\n return current file position\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("tell", 0);
+ __Pyx_RefNannySetupContext("tell");
__Pyx_TraceCall("tell", __pyx_f[0], 883);
- /* "pysam/csamtools.pyx":887
+ /* "csamtools.pyx":887
* return current file position
* '''
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":888
+ /* "csamtools.pyx":888
* '''
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":889
+ /* "csamtools.pyx":889
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam: # <<<<<<<<<<<<<<
* raise NotImplementedError("seek only available in bam files")
*
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":890
+ /* "csamtools.pyx":890
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":892
+ /* "csamtools.pyx":892
* raise NotImplementedError("seek only available in bam files")
*
* return bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
* def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(__pyx_v_self->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_20fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n\n If *until_eof* is given, all reads from the current file position will be returned\n in order as they are within the file. Using this option will also fetch unmapped reads.\n\n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed\n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":894
+ * return bam_tell( self.samfile.x.bam )
+ *
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_10fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n\n If *until_eof* is given, all reads from the current file position will be returned\n in order as they are within the file. Using this option will also fetch unmapped reads.\n\n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed\n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_until_eof = 0;
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ int __pyx_v_reopen;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_t_15;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch");
+ __Pyx_TraceCall("fetch", __pyx_f[0], 894);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
PyObject* values[6] = {0,0,0,0,0,0};
- /* "pysam/csamtools.pyx":895
+ /* "csamtools.pyx":895
*
* def fetch( self,
* reference = None, # <<<<<<<<<<<<<<
*/
values[0] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":896
+ /* "csamtools.pyx":896
* def fetch( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":897
+ /* "csamtools.pyx":897
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
*/
values[2] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":898
+ /* "csamtools.pyx":898
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
*/
values[3] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":899
+ /* "csamtools.pyx":899
* end = None,
* region = None,
* callback = None, # <<<<<<<<<<<<<<
values[5] = __pyx_k_54;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_20fetch(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_until_eof);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":894
- * return bam_tell( self.samfile.x.bam )
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof) {
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- int __pyx_v_reopen;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_t_15;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch", 0);
- __Pyx_TraceCall("fetch", __pyx_f[0], 894);
- /* "pysam/csamtools.pyx":924
+ /* "csamtools.pyx":924
* cdef int rtid, rstart, rend, has_coord
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":925
+ /* "csamtools.pyx":925
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":927
+ /* "csamtools.pyx":927
* raise ValueError( "I/O operation on closed file" )
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
* if self.isstream: reopen = False
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 4)) {
- if (size > 4) __Pyx_RaiseTooManyValuesError(4);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+ if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+ if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
- #else
- Py_ssize_t i;
- PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
- for (i=0; i < 4; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- *(temps[i]) = item;
- }
- #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
- PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
__pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- for (index=0; index < 4; index++) {
- PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(item);
- *(temps[index]) = item;
- }
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L5_unpacking_done;
- __pyx_L4_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_9 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rstart = __pyx_t_12;
__pyx_v_rend = __pyx_t_13;
- /* "pysam/csamtools.pyx":929
+ /* "csamtools.pyx":929
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*
* if self.isstream: reopen = False # <<<<<<<<<<<<<<
* else: reopen = True
*
*/
- if (__pyx_v_self->isstream) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) {
__pyx_v_reopen = 0;
- goto __pyx_L6;
+ goto __pyx_L9;
}
/*else*/ {
- /* "pysam/csamtools.pyx":930
+ /* "csamtools.pyx":930
*
* if self.isstream: reopen = False
* else: reopen = True # <<<<<<<<<<<<<<
*/
__pyx_v_reopen = 1;
}
- __pyx_L6:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":932
+ /* "csamtools.pyx":932
* else: reopen = True
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
- /* "pysam/csamtools.pyx":933
+ /* "csamtools.pyx":933
*
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_14 = (!__pyx_t_4);
if (__pyx_t_14) {
- __pyx_t_4 = (!__pyx_v_self->isremote);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
__pyx_t_15 = __pyx_t_4;
} else {
__pyx_t_15 = __pyx_t_14;
}
if (__pyx_t_14) {
- /* "pysam/csamtools.pyx":934
+ /* "csamtools.pyx":934
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
- /* "pysam/csamtools.pyx":936
+ /* "csamtools.pyx":936
* raise ValueError( "fetch called on bamfile without index" )
*
* if callback: # <<<<<<<<<<<<<<
__pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- /* "pysam/csamtools.pyx":937
+ /* "csamtools.pyx":937
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ goto __pyx_L13;
}
- __pyx_L10:;
+ __pyx_L13:;
- /* "pysam/csamtools.pyx":938
+ /* "csamtools.pyx":938
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* return bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ goto __pyx_L14;
}
- __pyx_L11:;
+ __pyx_L14:;
- /* "pysam/csamtools.pyx":939
+ /* "csamtools.pyx":939
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
* return bam_fetch(self.samfile.x.bam, # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
- /* "pysam/csamtools.pyx":945
+ /* "csamtools.pyx":945
* rend,
* <void*>callback,
* fetch_callback ) # <<<<<<<<<<<<<<
* else:
* if has_coord:
*/
- __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_5pysam_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L12;
}
/*else*/ {
- /* "pysam/csamtools.pyx":947
+ /* "csamtools.pyx":947
* fetch_callback )
* else:
* if has_coord: # <<<<<<<<<<<<<<
*/
if (__pyx_v_has_coord) {
- /* "pysam/csamtools.pyx":948
+ /* "csamtools.pyx":948
* else:
* if has_coord:
* return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen ) # <<<<<<<<<<<<<<
__pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7);
__Pyx_GOTREF(__pyx_t_7);
if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_r = __pyx_t_7;
__pyx_t_7 = 0;
goto __pyx_L0;
- goto __pyx_L12;
+ goto __pyx_L15;
}
/*else*/ {
- /* "pysam/csamtools.pyx":950
+ /* "csamtools.pyx":950
* return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
* else:
* if until_eof: # <<<<<<<<<<<<<<
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":951
+ /* "csamtools.pyx":951
* else:
* if until_eof:
* return IteratorRowAll( self, reopen=reopen ) # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
__pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L13;
+ goto __pyx_L16;
}
/*else*/ {
- /* "pysam/csamtools.pyx":954
+ /* "csamtools.pyx":954
* else:
* # AH: check - reason why no reopen for AllRefs?
* return IteratorRowAllRefs(self ) # , reopen=reopen ) # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_r = __pyx_t_6;
__pyx_t_6 = 0;
goto __pyx_L0;
}
- __pyx_L13:;
+ __pyx_L16:;
}
- __pyx_L12:;
+ __pyx_L15:;
}
- __pyx_L9:;
- goto __pyx_L7;
+ __pyx_L12:;
+ goto __pyx_L10;
}
/*else*/ {
- /* "pysam/csamtools.pyx":956
+ /* "csamtools.pyx":956
* return IteratorRowAllRefs(self ) # , reopen=reopen )
* else:
* if has_coord: # <<<<<<<<<<<<<<
*/
if (__pyx_v_has_coord) {
- /* "pysam/csamtools.pyx":957
+ /* "csamtools.pyx":957
* else:
* if has_coord:
* raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ goto __pyx_L17;
}
- __pyx_L14:;
+ __pyx_L17:;
- /* "pysam/csamtools.pyx":959
+ /* "csamtools.pyx":959
* raise ValueError ("fetching by region is not available for sam files" )
*
* if callback: # <<<<<<<<<<<<<<
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":960
+ /* "csamtools.pyx":960
*
* if callback:
* raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
+ goto __pyx_L18;
}
- __pyx_L15:;
+ __pyx_L18:;
- /* "pysam/csamtools.pyx":962
+ /* "csamtools.pyx":962
* raise NotImplementedError( "callback not implemented yet" )
*
* if self.samfile.header == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "fetch called for samfile without header")
*
*/
- __pyx_t_3 = (__pyx_v_self->samfile->header == NULL);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":963
+ /* "csamtools.pyx":963
*
* if self.samfile.header == NULL:
* raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ goto __pyx_L19;
}
- __pyx_L16:;
+ __pyx_L19:;
- /* "pysam/csamtools.pyx":967
+ /* "csamtools.pyx":967
* # check if targets are defined
* # give warning, sam_read1 segfaults
* if self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
* warnings.warn( "fetch called for samfile without header")
*
*/
- __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":968
+ /* "csamtools.pyx":968
* # give warning, sam_read1 segfaults
* if self.samfile.header.n_targets == 0:
* warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L17;
+ goto __pyx_L20;
}
- __pyx_L17:;
+ __pyx_L20:;
- /* "pysam/csamtools.pyx":970
+ /* "csamtools.pyx":970
* warnings.warn( "fetch called for samfile without header")
*
* return IteratorRowAll( self, reopen=reopen ) # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_7 = 0;
goto __pyx_L0;
}
- __pyx_L7:;
+ __pyx_L10:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_22mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("mate (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_22mate(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_read));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":972
+/* "csamtools.pyx":972
* return IteratorRowAll( self, reopen=reopen )
*
* def mate( self, # <<<<<<<<<<<<<<
* '''return the mate of :class:`AlignedRead` *read*.
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_11mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
uint32_t __pyx_v_flag;
- __pyx_t_5pysam_9csamtools_MateData __pyx_v_mate_data;
+ __pyx_t_9csamtools_MateData __pyx_v_mate_data;
int __pyx_v_x;
- struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_dest = 0;
+ struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- uint32_t __pyx_t_1;
- int __pyx_t_2;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- bam1_t *__pyx_t_5;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate", 0);
+ __Pyx_RefNannySetupContext("mate");
__Pyx_TraceCall("mate", __pyx_f[0], 972);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":985
+ /* "csamtools.pyx":985
*
* '''
* cdef uint32_t flag = read._delegate.core.flag # <<<<<<<<<<<<<<
*
* if flag & BAM_FPAIRED == 0:
*/
- __pyx_t_1 = __pyx_v_read->_delegate->core.flag;
- __pyx_v_flag = __pyx_t_1;
+ __pyx_v_flag = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.flag;
- /* "pysam/csamtools.pyx":987
+ /* "csamtools.pyx":987
* cdef uint32_t flag = read._delegate.core.flag
*
* if flag & BAM_FPAIRED == 0: # <<<<<<<<<<<<<<
* raise ValueError( "read %s: is unpaired" % (read.qname))
* if flag & BAM_FMUNMAP != 0:
*/
- __pyx_t_2 = ((__pyx_v_flag & 1) == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = ((__pyx_v_flag & 1) == 0);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":988
+ /* "csamtools.pyx":988
*
* if flag & BAM_FPAIRED == 0:
* raise ValueError( "read %s: is unpaired" % (read.qname)) # <<<<<<<<<<<<<<
* if flag & BAM_FMUNMAP != 0:
* raise ValueError( "mate %s: is unmapped" % (read.qname))
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_4, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":989
+ /* "csamtools.pyx":989
* if flag & BAM_FPAIRED == 0:
* raise ValueError( "read %s: is unpaired" % (read.qname))
* if flag & BAM_FMUNMAP != 0: # <<<<<<<<<<<<<<
* raise ValueError( "mate %s: is unmapped" % (read.qname))
*
*/
- __pyx_t_2 = ((__pyx_v_flag & 8) != 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = ((__pyx_v_flag & 8) != 0);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":990
+ /* "csamtools.pyx":990
* raise ValueError( "read %s: is unpaired" % (read.qname))
* if flag & BAM_FMUNMAP != 0:
* raise ValueError( "mate %s: is unmapped" % (read.qname)) # <<<<<<<<<<<<<<
*
* cdef MateData mate_data
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":994
+ /* "csamtools.pyx":994
* cdef MateData mate_data
*
* mate_data.name = <char *>bam1_qname(read._delegate) # <<<<<<<<<<<<<<
* mate_data.mate = NULL
* # xor flags to get the other mate
*/
- __pyx_v_mate_data.name = ((char *)bam1_qname(__pyx_v_read->_delegate));
+ __pyx_v_mate_data.name = ((char *)bam1_qname(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate));
- /* "pysam/csamtools.pyx":995
+ /* "csamtools.pyx":995
*
* mate_data.name = <char *>bam1_qname(read._delegate)
* mate_data.mate = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_mate_data.mate = NULL;
- /* "pysam/csamtools.pyx":997
+ /* "csamtools.pyx":997
* mate_data.mate = NULL
* # xor flags to get the other mate
* cdef int x = BAM_FREAD1 + BAM_FREAD2 # <<<<<<<<<<<<<<
*/
__pyx_v_x = 192;
- /* "pysam/csamtools.pyx":998
+ /* "csamtools.pyx":998
* # xor flags to get the other mate
* cdef int x = BAM_FREAD1 + BAM_FREAD2
* mate_data.flag = ( flag ^ x) & x # <<<<<<<<<<<<<<
*/
__pyx_v_mate_data.flag = ((__pyx_v_flag ^ __pyx_v_x) & __pyx_v_x);
- /* "pysam/csamtools.pyx":1006
+ /* "csamtools.pyx":1006
* read._delegate.core.mpos + 1,
* <void*>&mate_data,
* mate_callback ) # <<<<<<<<<<<<<<
*
* if mate_data.mate == NULL:
*/
- bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_5pysam_9csamtools_mate_callback);
+ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mtid, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos, (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback);
- /* "pysam/csamtools.pyx":1008
+ /* "csamtools.pyx":1008
* mate_callback )
*
* if mate_data.mate == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "mate not found" )
*
*/
- __pyx_t_2 = (__pyx_v_mate_data.mate == NULL);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_mate_data.mate == NULL);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1009
+ /* "csamtools.pyx":1009
*
* if mate_data.mate == NULL:
* raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_72), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_72), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":1011
+ /* "csamtools.pyx":1011
* raise ValueError( "mate not found" )
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
* dest._delegate = mate_data.mate
* return dest
*/
- __pyx_t_3 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (!(likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5pysam_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_2 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1012
+ /* "csamtools.pyx":1012
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = mate_data.mate # <<<<<<<<<<<<<<
* return dest
*
*/
- __pyx_t_5 = __pyx_v_mate_data.mate;
- __pyx_v_dest->_delegate = __pyx_t_5;
+ __pyx_v_dest->_delegate = __pyx_v_mate_data.mate;
- /* "pysam/csamtools.pyx":1013
+ /* "csamtools.pyx":1013
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = mate_data.mate
* return dest # <<<<<<<<<<<<<<
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.mate", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.mate", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_24count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1015
+ * return dest
+ *
+ * def count( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_12count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_until_eof = 0;
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_counter;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("count (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("count");
+ __Pyx_TraceCall("count", __pyx_f[0], 1015);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
PyObject* values[5] = {0,0,0,0,0};
- /* "pysam/csamtools.pyx":1016
+ /* "csamtools.pyx":1016
*
* def count( self,
* reference = None, # <<<<<<<<<<<<<<
*/
values[0] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1017
+ /* "csamtools.pyx":1017
* def count( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1018
+ /* "csamtools.pyx":1018
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
*/
values[2] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1019
+ /* "csamtools.pyx":1019
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
values[4] = __pyx_k_73;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("count", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_24count(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_until_eof);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1015
- * return dest
- *
- * def count( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof) {
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_counter;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count", 0);
- __Pyx_TraceCall("count", __pyx_f[0], 1015);
__Pyx_INCREF(__pyx_v_region);
- /* "pysam/csamtools.pyx":1033
+ /* "csamtools.pyx":1033
* cdef int rend
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1034
+ /* "csamtools.pyx":1034
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1036
+ /* "csamtools.pyx":1036
* raise ValueError( "I/O operation on closed file" )
*
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
* cdef int counter
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 4)) {
- if (size > 4) __Pyx_RaiseTooManyValuesError(4);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+ if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+ if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
- #else
- Py_ssize_t i;
- PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
- for (i=0; i < 4; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- *(temps[i]) = item;
- }
- #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
- PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
__pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- for (index=0; index < 4; index++) {
- PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(item);
- *(temps[index]) = item;
- }
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L5_unpacking_done;
- __pyx_L4_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_9 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_rstart = __pyx_t_11;
__pyx_v_rend = __pyx_t_12;
- /* "pysam/csamtools.pyx":1039
+ /* "csamtools.pyx":1039
*
* cdef int counter
* counter = 0; # <<<<<<<<<<<<<<
*/
__pyx_v_counter = 0;
- /* "pysam/csamtools.pyx":1041
+ /* "csamtools.pyx":1041
* counter = 0;
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
- /* "pysam/csamtools.pyx":1042
+ /* "csamtools.pyx":1042
*
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = (!__pyx_t_4);
if (__pyx_t_13) {
- __pyx_t_4 = (!__pyx_v_self->isremote);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
__pyx_t_14 = __pyx_t_4;
} else {
__pyx_t_14 = __pyx_t_13;
}
if (__pyx_t_13) {
- /* "pysam/csamtools.pyx":1043
+ /* "csamtools.pyx":1043
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":1045
+ /* "csamtools.pyx":1045
* raise ValueError( "fetch called on bamfile without index" )
*
* if not region: # <<<<<<<<<<<<<<
__pyx_t_3 = (!__pyx_t_13);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1046
+ /* "csamtools.pyx":1046
*
* if not region:
* raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
- /* "pysam/csamtools.pyx":1047
+ /* "csamtools.pyx":1047
* if not region:
* raise ValueError( "counting functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
- /* "pysam/csamtools.pyx":1054
+ /* "csamtools.pyx":1054
* rend,
* <void*>&counter,
* count_callback ) # <<<<<<<<<<<<<<
* return counter
* else:
*/
- bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_5pysam_9csamtools_count_callback);
+ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback);
- /* "pysam/csamtools.pyx":1055
+ /* "csamtools.pyx":1055
* <void*>&counter,
* count_callback )
* return counter # <<<<<<<<<<<<<<
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L9;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1057
+ /* "csamtools.pyx":1057
* return counter
* else:
* raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L6:;
+ __pyx_L9:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_region);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_26pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed\n for each column within the :term:`region`.\n\n Note that :term:`SAM` formatted files do not allow random access.\n In these files, if a *region* or *reference* are given an exception is raised.\n\n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances.\n Possible options for the stepper are\n\n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask if mask=True.\n\n max_depth\n Maximum read depth permitted. The default limit is *8000*.\n\n truncate\n By default, the samtools pileup engine outputs all reads overlapping a region (see note below).\n If truncate is True and a region is given, only output columns in the exact region\n specificied.\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the\n first base of the first read *not* necessarily the first base of the region used in the query.\n\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1059
+ * raise ValueError ("count for a region is not available for sam files" )
+ *
+ * def pileup( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_13pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed\n for each column within the :term:`region`.\n\n Note that :term:`SAM` formatted files do not allow random access.\n In these files, if a *region* or *reference* are given an exception is raised.\n\n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances.\n Possible options for the stepper are\n\n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask if mask=True.\n\n max_depth\n Maximum read depth permitted. The default limit is *8000*.\n\n truncate\n By default, the samtools pileup engine outputs all reads overlapping a region (see note below).\n If truncate is True and a region is given, only output columns in the exact region\n specificied.\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the\n first base of the first read *not* necessarily the first base of the region used in the query.\n\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_kwargs = 0;
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ bam_plbuf_t *__pyx_v_buf;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("pileup (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("pileup");
+ __Pyx_TraceCall("pileup", __pyx_f[0], 1059);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL;
__Pyx_GOTREF(__pyx_v_kwargs);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
PyObject* values[5] = {0,0,0,0,0};
- /* "pysam/csamtools.pyx":1060
+ /* "csamtools.pyx":1060
*
* def pileup( self,
* reference = None, # <<<<<<<<<<<<<<
*/
values[0] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1061
+ /* "csamtools.pyx":1061
* def pileup( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1062
+ /* "csamtools.pyx":1062
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
*/
values[2] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1063
+ /* "csamtools.pyx":1063
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
*/
values[3] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1064
+ /* "csamtools.pyx":1064
* end = None,
* region = None,
* callback = None, # <<<<<<<<<<<<<<
values[4] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("pysam.csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_26pileup(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_kwargs);
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1059
- * raise ValueError ("count for a region is not available for sam files" )
- *
- * def pileup( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs) {
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- bam_plbuf_t *__pyx_v_buf;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup", 0);
- __Pyx_TraceCall("pileup", __pyx_f[0], 1059);
-
- /* "pysam/csamtools.pyx":1115
+ /* "csamtools.pyx":1115
* cdef bam_plbuf_t *buf
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1116
+ /* "csamtools.pyx":1116
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1118
+ /* "csamtools.pyx":1118
* raise ValueError( "I/O operation on closed file" )
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
* if self.isbam:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 4)) {
- if (size > 4) __Pyx_RaiseTooManyValuesError(4);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
+ if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
+ if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
- #else
- Py_ssize_t i;
- PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
- for (i=0; i < 4; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- *(temps[i]) = item;
- }
- #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
- PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
__pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- for (index=0; index < 4; index++) {
- PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(item);
- *(temps[index]) = item;
- }
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L5_unpacking_done;
- __pyx_L4_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_9 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rstart = __pyx_t_12;
__pyx_v_rend = __pyx_t_13;
- /* "pysam/csamtools.pyx":1120
+ /* "csamtools.pyx":1120
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
*
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
- /* "pysam/csamtools.pyx":1121
+ /* "csamtools.pyx":1121
*
* if self.isbam:
* if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":1123
+ /* "csamtools.pyx":1123
* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
*
* if callback: # <<<<<<<<<<<<<<
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1124
+ /* "csamtools.pyx":1124
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
- /* "pysam/csamtools.pyx":1126
+ /* "csamtools.pyx":1126
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
*
* buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
* self.index, rtid, rstart, rend,
*/
- __pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_5pysam_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
+ __pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
- /* "pysam/csamtools.pyx":1129
+ /* "csamtools.pyx":1129
* bam_fetch(self.samfile.x.bam,
* self.index, rtid, rstart, rend,
* buf, pileup_fetch_callback ) # <<<<<<<<<<<<<<
*
* # finalize pileup
*/
- bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_5pysam_9csamtools_pileup_fetch_callback);
+ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback);
- /* "pysam/csamtools.pyx":1132
+ /* "csamtools.pyx":1132
*
* # finalize pileup
* bam_plbuf_push( NULL, buf) # <<<<<<<<<<<<<<
*/
bam_plbuf_push(NULL, __pyx_v_buf);
- /* "pysam/csamtools.pyx":1133
+ /* "csamtools.pyx":1133
* # finalize pileup
* bam_plbuf_push( NULL, buf)
* bam_plbuf_destroy(buf) # <<<<<<<<<<<<<<
* if has_coord:
*/
bam_plbuf_destroy(__pyx_v_buf);
- goto __pyx_L8;
+ goto __pyx_L11;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1135
+ /* "csamtools.pyx":1135
* bam_plbuf_destroy(buf)
* else:
* if has_coord: # <<<<<<<<<<<<<<
*/
if (__pyx_v_has_coord) {
- /* "pysam/csamtools.pyx":1136
+ /* "csamtools.pyx":1136
* else:
* if has_coord:
* return IteratorColumnRegion( self, # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
-
- /* "pysam/csamtools.pyx":1140
- * start = rstart,
- * end = rend,
- * **kwargs ) # <<<<<<<<<<<<<<
- * else:
- * return IteratorColumnAllRefs(self, **kwargs )
- */
- __pyx_t_5 = PyDict_Copy(((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- /* "pysam/csamtools.pyx":1137
+ /* "csamtools.pyx":1137
* if has_coord:
* return IteratorColumnRegion( self,
* tid = rtid, # <<<<<<<<<<<<<<
*/
__pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid)))) {
- __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__tid)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":1138
+ /* "csamtools.pyx":1138
* return IteratorColumnRegion( self,
* tid = rtid,
* start = rstart, # <<<<<<<<<<<<<<
*/
__pyx_t_6 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start)))) {
- __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__start)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":1139
+ /* "csamtools.pyx":1139
* tid = rtid,
* start = rstart,
* end = rend, # <<<<<<<<<<<<<<
*/
__pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end)))) {
- __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__end)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":1140
+ * start = rstart,
+ * end = rend,
+ * **kwargs ) # <<<<<<<<<<<<<<
+ * else:
+ * return IteratorColumnAllRefs(self, **kwargs )
+ */
+ if (PyDict_Update(((PyObject *)__pyx_t_5), ((PyObject *)__pyx_v_kwargs)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_r = __pyx_t_6;
__pyx_t_6 = 0;
goto __pyx_L0;
- goto __pyx_L10;
+ goto __pyx_L13;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1142
+ /* "csamtools.pyx":1142
* **kwargs )
* else:
* return IteratorColumnAllRefs(self, **kwargs ) # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_5 = ((PyObject *)__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
+ __pyx_t_5 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_r = __pyx_t_5;
+ __pyx_t_5 = 0;
goto __pyx_L0;
}
- __pyx_L10:;
+ __pyx_L13:;
}
- __pyx_L8:;
- goto __pyx_L6;
+ __pyx_L11:;
+ goto __pyx_L9;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1145
+ /* "csamtools.pyx":1145
*
* else:
* raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
*
* def close( self ):
*/
- __pyx_t_7 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L6:;
+ __pyx_L9:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_28close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("close (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_28close(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1147
+/* "csamtools.pyx":1147
* raise NotImplementedError( "pileup of samfiles not implemented yet" )
*
* def close( self ): # <<<<<<<<<<<<<<
* closes the :class:`pysam.Samfile`.'''
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_28close(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_14close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_RefNannySetupContext("close");
__Pyx_TraceCall("close", __pyx_f[0], 1147);
- /* "pysam/csamtools.pyx":1150
+ /* "csamtools.pyx":1150
* '''
* closes the :class:`pysam.Samfile`.'''
* if self.samfile != NULL: # <<<<<<<<<<<<<<
* samclose( self.samfile )
* bam_index_destroy(self.index);
*/
- __pyx_t_1 = (__pyx_v_self->samfile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1151
+ /* "csamtools.pyx":1151
* closes the :class:`pysam.Samfile`.'''
* if self.samfile != NULL:
* samclose( self.samfile ) # <<<<<<<<<<<<<<
* bam_index_destroy(self.index);
* self.samfile = NULL
*/
- samclose(__pyx_v_self->samfile);
+ samclose(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile);
- /* "pysam/csamtools.pyx":1152
+ /* "csamtools.pyx":1152
* if self.samfile != NULL:
* samclose( self.samfile )
* bam_index_destroy(self.index); # <<<<<<<<<<<<<<
* self.samfile = NULL
*
*/
- bam_index_destroy(__pyx_v_self->index);
+ bam_index_destroy(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index);
- /* "pysam/csamtools.pyx":1153
+ /* "csamtools.pyx":1153
* samclose( self.samfile )
* bam_index_destroy(self.index);
* self.samfile = NULL # <<<<<<<<<<<<<<
*
* def __dealloc__( self ):
*/
- __pyx_v_self->samfile = NULL;
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":1155
+/* "csamtools.pyx":1155
* self.samfile = NULL
*
* def __dealloc__( self ): # <<<<<<<<<<<<<<
* # note: no doc string
*/
-static void __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1155);
- /* "pysam/csamtools.pyx":1159
+ /* "csamtools.pyx":1159
* # note: no doc string
* # note: __del__ is not called.
* self.close() # <<<<<<<<<<<<<<
* bam_destroy1(self.b)
* if self._filename != NULL: free( self._filename )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1160
+ /* "csamtools.pyx":1160
* # note: __del__ is not called.
* self.close()
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self._filename != NULL: free( self._filename )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1161
+ /* "csamtools.pyx":1161
* self.close()
* bam_destroy1(self.b)
* if self._filename != NULL: free( self._filename ) # <<<<<<<<<<<<<<
*
* cpdef int write( self, AlignedRead read ) except -1:
*/
- __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_3) {
- free(__pyx_v_self->_filename);
- goto __pyx_L3;
+ free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "pysam/csamtools.pyx":1163
+/* "csamtools.pyx":1163
* if self._filename != NULL: free( self._filename )
*
* cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
* write a single :class:`pysam.AlignedRead` to disk.
*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static int __pyx_f_5pysam_9csamtools_7Samfile_write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_RefNannySetupContext("write");
__Pyx_TraceCall("write", __pyx_f[0], 1163);
/* Check if called by wrapper */
if (unlikely(__pyx_skip_dispatch)) ;
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_33write)) {
+ if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (void *)&__pyx_pf_9csamtools_7Samfile_16write)) {
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(((PyObject *)__pyx_v_read));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_read));
__Pyx_GIVEREF(((PyObject *)__pyx_v_read));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "pysam/csamtools.pyx":1169
+ /* "csamtools.pyx":1169
* returns the number of bytes written.
* '''
* if not self._isOpen(): # <<<<<<<<<<<<<<
__pyx_t_6 = (!__pyx_t_5);
if (__pyx_t_6) {
- /* "pysam/csamtools.pyx":1170
+ /* "csamtools.pyx":1170
* '''
* if not self._isOpen():
* return 0 # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1172
+ /* "csamtools.pyx":1172
* return 0
*
* return samwrite( self.samfile, read._delegate ) # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_WriteUnraisable("pysam.csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_32write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("write (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_32write(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_read));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1163
+/* "csamtools.pyx":1163
* if self._filename != NULL: free( self._filename )
*
* cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
* write a single :class:`pysam.AlignedRead` to disk.
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_32write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_16write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_RefNannySetupContext("write");
__Pyx_TraceCall("write", __pyx_f[0], 1163);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->write(__pyx_v_self, __pyx_v_read, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read), 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_34__enter__[] = "Samfile.__enter__(self)";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__enter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1174
+/* "csamtools.pyx":1174
* return samwrite( self.samfile, read._delegate )
*
* def __enter__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_17__enter__[] = "Samfile.__enter__(self)";
+static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__enter__", 0);
+ __Pyx_RefNannySetupContext("__enter__");
__Pyx_TraceCall("__enter__", __pyx_f[0], 1174);
- /* "pysam/csamtools.pyx":1175
+ /* "csamtools.pyx":1175
*
* def __enter__(self):
* return self # <<<<<<<<<<<<<<
* def __exit__(self, exc_type, exc_value, traceback):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_36__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- CYTHON_UNUSED PyObject *__pyx_v_exc_type = 0;
- CYTHON_UNUSED PyObject *__pyx_v_exc_value = 0;
- CYTHON_UNUSED PyObject *__pyx_v_traceback = 0;
- PyObject *__pyx_r = 0;
+/* "csamtools.pyx":1177
+ * return self
+ *
+ * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
+ * self.close()
+ * return False
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_18__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
+static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_exc_type = 0;
+ PyObject *__pyx_v_exc_value = 0;
+ PyObject *__pyx_v_traceback = 0;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__exit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__exit__");
+ __Pyx_TraceCall("__exit__", __pyx_f[0], 1177);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_value)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_value);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__traceback)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__traceback);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_exc_type, __pyx_v_exc_value, __pyx_v_traceback);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-/* "pysam/csamtools.pyx":1177
- * return self
- *
- * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
- * self.close()
- * return False
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__exit__", 0);
- __Pyx_TraceCall("__exit__", __pyx_f[0], 1177);
-
- /* "pysam/csamtools.pyx":1178
+ /* "csamtools.pyx":1178
*
* def __exit__(self, exc_type, exc_value, traceback):
* self.close() # <<<<<<<<<<<<<<
* return False
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1179
+ /* "csamtools.pyx":1179
* def __exit__(self, exc_type, exc_value, traceback):
* self.close()
* return False # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1188
+/* "csamtools.pyx":1188
* property filename:
* '''number of :term:`filename` associated with this object.'''
* def __get__(self): # <<<<<<<<<<<<<<
* return self._filename
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1188);
- /* "pysam/csamtools.pyx":1189
+ /* "csamtools.pyx":1189
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self._filename
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1190
+ /* "csamtools.pyx":1190
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return self._filename # <<<<<<<<<<<<<<
* property nreferences:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1194
+/* "csamtools.pyx":1194
* property nreferences:
* '''number of :term:`reference` sequences in the file.'''
* def __get__(self): # <<<<<<<<<<<<<<
* return self.samfile.header.n_targets
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1194);
- /* "pysam/csamtools.pyx":1195
+ /* "csamtools.pyx":1195
* '''number of :term:`reference` sequences in the file.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self.samfile.header.n_targets
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1196
+ /* "csamtools.pyx":1196
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return self.samfile.header.n_targets # <<<<<<<<<<<<<<
* property references:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.nreferences.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.nreferences.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1200
+/* "csamtools.pyx":1200
* property references:
* """tuple with the names of :term:`reference` sequences."""
* def __get__(self): # <<<<<<<<<<<<<<
* t = []
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
PyObject *__pyx_r = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1200);
- /* "pysam/csamtools.pyx":1201
+ /* "csamtools.pyx":1201
* """tuple with the names of :term:`reference` sequences."""
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1202
+ /* "csamtools.pyx":1202
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = [] # <<<<<<<<<<<<<<
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1203
+ /* "csamtools.pyx":1203
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = []
* for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
* return tuple(t)
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":1204
+ /* "csamtools.pyx":1204
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) ) # <<<<<<<<<<<<<<
* return tuple(t)
*
*/
- __pyx_t_2 = __pyx_f_5pysam_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- /* "pysam/csamtools.pyx":1205
+ /* "csamtools.pyx":1205
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
* return tuple(t) # <<<<<<<<<<<<<<
* property lengths:
*/
__Pyx_XDECREF(__pyx_r);
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.references.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.references.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_t);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1211
+/* "csamtools.pyx":1211
* :attr:`pysam.Samfile.references`
* """
* def __get__(self): # <<<<<<<<<<<<<<
* t = []
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
PyObject *__pyx_r = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1211);
- /* "pysam/csamtools.pyx":1212
+ /* "csamtools.pyx":1212
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1213
+ /* "csamtools.pyx":1213
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = [] # <<<<<<<<<<<<<<
* t.append( self.samfile.header.target_len[x] )
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1214
+ /* "csamtools.pyx":1214
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = []
* for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* t.append( self.samfile.header.target_len[x] )
* return tuple(t)
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":1215
+ /* "csamtools.pyx":1215
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( self.samfile.header.target_len[x] ) # <<<<<<<<<<<<<<
* return tuple(t)
*
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((__pyx_v_self->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- /* "pysam/csamtools.pyx":1216
+ /* "csamtools.pyx":1216
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( self.samfile.header.target_len[x] )
* return tuple(t) # <<<<<<<<<<<<<<
* property mapped:
*/
__Pyx_XDECREF(__pyx_r);
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.lengths.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.lengths.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_t);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1221
+/* "csamtools.pyx":1221
* """total number of mapped reads in file.
* """
* def __get__(self): # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self) {
int __pyx_v_tid;
uint32_t __pyx_v_total;
PyObject *__pyx_r = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1221);
- /* "pysam/csamtools.pyx":1222
+ /* "csamtools.pyx":1222
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1223
+ /* "csamtools.pyx":1223
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
*
* cdef int tid
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
__pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_93), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1226
+ /* "csamtools.pyx":1226
*
* cdef int tid
* cdef uint32_t total = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_total = 0;
- /* "pysam/csamtools.pyx":1227
+ /* "csamtools.pyx":1227
* cdef int tid
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* total += pysam_get_mapped( self.index, tid )
* return total
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
- /* "pysam/csamtools.pyx":1228
+ /* "csamtools.pyx":1228
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets:
* total += pysam_get_mapped( self.index, tid ) # <<<<<<<<<<<<<<
* return total
*
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_mapped(__pyx_v_self->index, __pyx_v_tid));
+ __pyx_v_total = (__pyx_v_total + pysam_get_mapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid));
}
- /* "pysam/csamtools.pyx":1229
+ /* "csamtools.pyx":1229
* for tid from 0 <= tid < self.samfile.header.n_targets:
* total += pysam_get_mapped( self.index, tid )
* return total # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.mapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.mapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1234
+/* "csamtools.pyx":1234
* """total number of unmapped reads in file.
* """
* def __get__(self): # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self) {
int __pyx_v_tid;
uint32_t __pyx_v_total;
PyObject *__pyx_r = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1234);
- /* "pysam/csamtools.pyx":1235
+ /* "csamtools.pyx":1235
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
* cdef int tid
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1236
+ /* "csamtools.pyx":1236
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
* cdef int tid
* cdef uint32_t total = 0
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
__pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_96), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1238
+ /* "csamtools.pyx":1238
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
* cdef int tid
* cdef uint32_t total = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_total = 0;
- /* "pysam/csamtools.pyx":1239
+ /* "csamtools.pyx":1239
* cdef int tid
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* total += pysam_get_unmapped( self.index, tid )
* # get unmapped reads without coordinates
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
- /* "pysam/csamtools.pyx":1240
+ /* "csamtools.pyx":1240
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets:
* total += pysam_get_unmapped( self.index, tid ) # <<<<<<<<<<<<<<
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 )
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, __pyx_v_tid));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid));
}
- /* "pysam/csamtools.pyx":1242
+ /* "csamtools.pyx":1242
* total += pysam_get_unmapped( self.index, tid )
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 ) # <<<<<<<<<<<<<<
* return total
*
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, -1));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, -1));
- /* "pysam/csamtools.pyx":1243
+ /* "csamtools.pyx":1243
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 )
* return total # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1247
+/* "csamtools.pyx":1247
* property text:
* '''full contents of the :term:`sam file` header as a string.'''
* def __get__(self): # <<<<<<<<<<<<<<
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1247);
- /* "pysam/csamtools.pyx":1248
+ /* "csamtools.pyx":1248
* '''full contents of the :term:`sam file` header as a string.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1249
+ /* "csamtools.pyx":1249
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) # <<<<<<<<<<<<<<
* property header:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_from_string_and_size(__pyx_v_self->samfile->header->text, __pyx_v_self->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.text.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.text.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1255
+/* "csamtools.pyx":1255
* a two-level dictionary.
* '''
* def __get__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_result = NULL;
PyObject *__pyx_v_t = NULL;
PyObject *__pyx_v_line = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1255);
- /* "pysam/csamtools.pyx":1256
+ /* "csamtools.pyx":1256
* '''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* result = {}
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1258
+ /* "csamtools.pyx":1258
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
*
* result = {} # <<<<<<<<<<<<<<
__pyx_v_result = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1260
+ /* "csamtools.pyx":1260
* result = {}
*
* if self.samfile.header.text != NULL: # <<<<<<<<<<<<<<
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
*/
- __pyx_t_4 = (__pyx_v_self->samfile->header->text != NULL);
+ __pyx_t_4 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text != NULL);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1262
+ /* "csamtools.pyx":1262
* if self.samfile.header.text != NULL:
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text # <<<<<<<<<<<<<<
* for line in t.split("\n"):
* if not line.strip(): continue
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1263
+ /* "csamtools.pyx":1263
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
* for line in t.split("\n"): # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
} else {
__pyx_t_1 = __pyx_t_6(__pyx_t_2);
if (unlikely(!__pyx_t_1)) {
__pyx_v_line = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1264
+ /* "csamtools.pyx":1264
* t = self.text
* for line in t.split("\n"):
* if not line.strip(): continue # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- goto __pyx_L5_continue;
- goto __pyx_L7;
+ goto __pyx_L7_continue;
+ goto __pyx_L9;
}
- __pyx_L7:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":1265
+ /* "csamtools.pyx":1265
* for line in t.split("\n"):
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
}
#endif
- /* "pysam/csamtools.pyx":1266
+ /* "csamtools.pyx":1266
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t") # <<<<<<<<<<<<<<
__pyx_v_fields = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1267
+ /* "csamtools.pyx":1267
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t")
* record = fields[0] # <<<<<<<<<<<<<<
__pyx_v_record = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1268
+ /* "csamtools.pyx":1268
* fields = line[1:].split("\t")
* record = fields[0]
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line) # <<<<<<<<<<<<<<
#ifndef CYTHON_WITHOUT_ASSERTIONS
__pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(!__pyx_t_3)) {
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
}
#endif
- /* "pysam/csamtools.pyx":1271
+ /* "csamtools.pyx":1271
*
* # treat comments
* if record == "CO": # <<<<<<<<<<<<<<
* if record not in result: result[record] = []
* result[record].append( "\t".join( fields[1:] ) )
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1272
+ /* "csamtools.pyx":1272
* # treat comments
* if record == "CO":
* if record not in result: result[record] = [] # <<<<<<<<<<<<<<
* result[record].append( "\t".join( fields[1:] ) )
* continue
*/
- __pyx_t_3 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_3 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L9;
+ goto __pyx_L11;
}
- __pyx_L9:;
+ __pyx_L11:;
- /* "pysam/csamtools.pyx":1273
+ /* "csamtools.pyx":1273
* if record == "CO":
* if record not in result: result[record] = []
* result[record].append( "\t".join( fields[1:] ) ) # <<<<<<<<<<<<<<
__pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":1274
+ /* "csamtools.pyx":1274
* if record not in result: result[record] = []
* result[record].append( "\t".join( fields[1:] ) )
* continue # <<<<<<<<<<<<<<
*
* # the following is clumsy as generators do not work?
*/
- goto __pyx_L5_continue;
- goto __pyx_L8;
+ goto __pyx_L7_continue;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":1277
+ /* "csamtools.pyx":1277
*
* # the following is clumsy as generators do not work?
* x = {} # <<<<<<<<<<<<<<
__pyx_v_x = __pyx_t_9;
__pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":1278
+ /* "csamtools.pyx":1278
* # the following is clumsy as generators do not work?
* x = {}
* for field in fields[1:]: # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_8)) {
+ if (PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
+ } else if (PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
} else {
__pyx_t_9 = __pyx_t_11(__pyx_t_8);
if (unlikely(!__pyx_t_9)) {
__pyx_v_field = __pyx_t_9;
__pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":1279
+ /* "csamtools.pyx":1279
* x = {}
* for field in fields[1:]:
* key, value = field.split(":",1) # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
PyObject* sequence = __pyx_t_7;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_9 = PyList_GET_ITEM(sequence, 0);
__pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_1);
- #else
- __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_12 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L12_unpacking_failed;
+ index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L14_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
+ index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L14_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- goto __pyx_L13_unpacking_done;
- __pyx_L12_unpacking_failed:;
+ goto __pyx_L15_unpacking_done;
+ __pyx_L14_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_13 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L13_unpacking_done:;
+ __pyx_L15_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_key);
__pyx_v_key = __pyx_t_9;
__pyx_v_value = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1282
+ /* "csamtools.pyx":1282
* # uppercase keys must be valid
* # lowercase are permitted for user fields
* if key in VALID_HEADER_FIELDS[record]: # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_record); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1283
+ /* "csamtools.pyx":1283
* # lowercase are permitted for user fields
* if key in VALID_HEADER_FIELDS[record]:
* x[key] = VALID_HEADER_FIELDS[record][key](value) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L14;
+ goto __pyx_L16;
}
- /* "pysam/csamtools.pyx":1284
+ /* "csamtools.pyx":1284
* if key in VALID_HEADER_FIELDS[record]:
* x[key] = VALID_HEADER_FIELDS[record][key](value)
* elif not key.isupper(): # <<<<<<<<<<<<<<
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1285
+ /* "csamtools.pyx":1285
* x[key] = VALID_HEADER_FIELDS[record][key](value)
* elif not key.isupper():
* x[key] = value # <<<<<<<<<<<<<<
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ goto __pyx_L16;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1287
+ /* "csamtools.pyx":1287
* x[key] = value
* else:
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) ) # <<<<<<<<<<<<<<
* if VALID_HEADER_TYPES[record] == dict:
*/
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L14:;
+ __pyx_L16:;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":1289
+ /* "csamtools.pyx":1289
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
*
* if VALID_HEADER_TYPES[record] == dict: # <<<<<<<<<<<<<<
__pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyDict_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyDict_Type))), Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1290
+ /* "csamtools.pyx":1290
*
* if VALID_HEADER_TYPES[record] == dict:
* if record in result: # <<<<<<<<<<<<<<
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x
*/
- __pyx_t_4 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_4 = ((PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1291
+ /* "csamtools.pyx":1291
* if VALID_HEADER_TYPES[record] == dict:
* if record in result:
* raise ValueError( "multiple '%s' lines are not permitted" % record ) # <<<<<<<<<<<<<<
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ goto __pyx_L18;
}
- __pyx_L16:;
+ __pyx_L18:;
- /* "pysam/csamtools.pyx":1292
+ /* "csamtools.pyx":1292
* if record in result:
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x # <<<<<<<<<<<<<<
* if record not in result: result[record] = []
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
+ goto __pyx_L17;
}
- /* "pysam/csamtools.pyx":1293
+ /* "csamtools.pyx":1293
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x
* elif VALID_HEADER_TYPES[record] == list: # <<<<<<<<<<<<<<
__pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyList_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyList_Type))), Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1294
+ /* "csamtools.pyx":1294
* result[record] = x
* elif VALID_HEADER_TYPES[record] == list:
* if record not in result: result[record] = [] # <<<<<<<<<<<<<<
* result[record].append( x )
*
*/
- __pyx_t_4 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
__pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- goto __pyx_L17;
+ goto __pyx_L19;
}
- __pyx_L17:;
+ __pyx_L19:;
- /* "pysam/csamtools.pyx":1295
+ /* "csamtools.pyx":1295
* elif VALID_HEADER_TYPES[record] == list:
* if record not in result: result[record] = []
* result[record].append( x ) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L15;
+ goto __pyx_L17;
}
- __pyx_L15:;
- __pyx_L5_continue:;
+ __pyx_L17:;
+ __pyx_L7_continue:;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1303
+ /* "csamtools.pyx":1303
* # SQ lines, the SQ information is not part of the textual header and thus
* # are missing from the output. See issue 84.
* if "SQ" not in result: # <<<<<<<<<<<<<<
* sq = []
* for ref, length in zip( self.references, self.lengths ):
*/
- __pyx_t_4 = (__Pyx_PyDict_Contains(((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1304
+ /* "csamtools.pyx":1304
* # are missing from the output. See issue 84.
* if "SQ" not in result:
* sq = [] # <<<<<<<<<<<<<<
* sq.append( {'LN': length, 'SN': ref } )
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_sq = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1305
+ /* "csamtools.pyx":1305
* if "SQ" not in result:
* sq = []
* for ref, length in zip( self.references, self.lengths ): # <<<<<<<<<<<<<<
* sq.append( {'LN': length, 'SN': ref } )
* result["SQ"] = sq
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_9);
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_8)) {
+ if (PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_8)) {
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
+ } else if (PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
} else {
__pyx_t_9 = __pyx_t_6(__pyx_t_8);
if (unlikely(!__pyx_t_9)) {
}
if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = PyList_GET_ITEM(sequence, 0);
__pyx_t_7 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_7);
- #else
- __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L21_unpacking_failed;
+ index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L23_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L21_unpacking_failed;
+ index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L23_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_1), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L22_unpacking_done;
- __pyx_L21_unpacking_failed:;
+ goto __pyx_L24_unpacking_done;
+ __pyx_L23_unpacking_failed:;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_13 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L22_unpacking_done:;
+ __pyx_L24_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_2;
__pyx_v_length = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1306
+ /* "csamtools.pyx":1306
* sq = []
* for ref, length in zip( self.references, self.lengths ):
* sq.append( {'LN': length, 'SN': ref } ) # <<<<<<<<<<<<<<
* result["SQ"] = sq
*
*/
+ if (unlikely(((PyObject *)__pyx_v_sq) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__LN), __pyx_v_length) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":1307
+ /* "csamtools.pyx":1307
* for ref, length in zip( self.references, self.lengths ):
* sq.append( {'LN': length, 'SN': ref } )
* result["SQ"] = sq # <<<<<<<<<<<<<<
* return result
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_sq)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L18;
+ goto __pyx_L20;
}
- __pyx_L18:;
- goto __pyx_L4;
+ __pyx_L20:;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1309
+ /* "csamtools.pyx":1309
* result["SQ"] = sq
*
* return result # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_12);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_38_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1311
+ * return result
+ *
+ * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
+ * '''build a header line from *fields* dictionary for *record*'''
+ *
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_19_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
+static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_fields = 0;
PyObject *__pyx_v_record = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_line = NULL;
+ PyObject *__pyx_v_key = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_buildLine (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_buildLine");
+ __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_fields, __pyx_v_record);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-/* "pysam/csamtools.pyx":1311
- * return result
- *
- * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
- * '''build a header line from *fields* dictionary for *record*'''
- *
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record) {
- PyObject *__pyx_v_line = NULL;
- PyObject *__pyx_v_key = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- PyObject *(*__pyx_t_6)(PyObject *);
- PyObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildLine", 0);
- __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311);
-
- /* "pysam/csamtools.pyx":1315
+ /* "csamtools.pyx":1315
*
* # TODO: add checking for field and sort order
* line = ["@%s" % record ] # <<<<<<<<<<<<<<
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_109), __pyx_v_record); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
__pyx_v_line = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1317
+ /* "csamtools.pyx":1317
* line = ["@%s" % record ]
* # comment
* if record == "CO": # <<<<<<<<<<<<<<
* line.append( fields )
* # user tags
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1318
+ /* "csamtools.pyx":1318
* # comment
* if record == "CO":
* line.append( fields ) # <<<<<<<<<<<<<<
* # user tags
* elif record.islower():
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = PyList_Append(__pyx_v_line, __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":1320
+ /* "csamtools.pyx":1320
* line.append( fields )
* # user tags
* elif record.islower(): # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1321
+ /* "csamtools.pyx":1321
* # user tags
* elif record.islower():
* for key in sorted(fields): # <<<<<<<<<<<<<<
* # defined tags
*/
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1322
+ /* "csamtools.pyx":1322
* elif record.islower():
* for key in sorted(fields):
* line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
* # defined tags
* else:
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L3;
+ goto __pyx_L6;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1326
+ /* "csamtools.pyx":1326
* else:
* # write fields of the specification
* for key in VALID_HEADER_ORDER[record]: # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1327
+ /* "csamtools.pyx":1327
* # write fields of the specification
* for key in VALID_HEADER_ORDER[record]:
* if key in fields: # <<<<<<<<<<<<<<
* line.append( "%s:%s" % (key, str(fields[key])))
* # write user fields
*/
- __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_v_fields, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PySequence_Contains(__pyx_v_fields, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1328
+ /* "csamtools.pyx":1328
* for key in VALID_HEADER_ORDER[record]:
* if key in fields:
* line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
* # write user fields
* for key in fields:
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1330
+ /* "csamtools.pyx":1330
* line.append( "%s:%s" % (key, str(fields[key])))
* # write user fields
* for key in fields: # <<<<<<<<<<<<<<
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1331
+ /* "csamtools.pyx":1331
* # write user fields
* for key in fields:
* if not key.isupper(): # <<<<<<<<<<<<<<
__pyx_t_8 = (!__pyx_t_3);
if (__pyx_t_8) {
- /* "pysam/csamtools.pyx":1332
+ /* "csamtools.pyx":1332
* for key in fields:
* if not key.isupper():
* line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
*
* return "\t".join( line )
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_7 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L11;
+ goto __pyx_L14;
}
- __pyx_L11:;
+ __pyx_L14:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1334
+ /* "csamtools.pyx":1334
* line.append( "%s:%s" % (key, str(fields[key])))
*
* return "\t".join( line ) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(((PyObject *)__pyx_v_line));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_line));
__Pyx_GIVEREF(((PyObject *)__pyx_v_line));
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_AddTraceback("pysam.csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_line);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1336
+/* "csamtools.pyx":1336
* return "\t".join( line )
*
* cdef bam_header_t * _buildHeader( self, new_header ): # <<<<<<<<<<<<<<
*
*/
-static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_new_header) {
+static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_new_header) {
PyObject *__pyx_v_lines = NULL;
bam_header_t *__pyx_v_dest;
PyObject *__pyx_v_record = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildHeader", 0);
+ __Pyx_RefNannySetupContext("_buildHeader");
__Pyx_TraceCall("_buildHeader", __pyx_f[0], 1336);
- /* "pysam/csamtools.pyx":1342
+ /* "csamtools.pyx":1342
* '''
*
* lines = [] # <<<<<<<<<<<<<<
* # check if hash exists
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_lines = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1349
+ /* "csamtools.pyx":1349
* cdef bam_header_t * dest
*
* dest = bam_header_init() # <<<<<<<<<<<<<<
*/
__pyx_v_dest = bam_header_init();
- /* "pysam/csamtools.pyx":1352
+ /* "csamtools.pyx":1352
*
* # first: defined tags
* for record in VALID_HEADERS: # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
} else {
__pyx_t_1 = __pyx_t_4(__pyx_t_2);
if (unlikely(!__pyx_t_1)) {
__pyx_v_record = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1353
+ /* "csamtools.pyx":1353
* # first: defined tags
* for record in VALID_HEADERS:
* if record in new_header: # <<<<<<<<<<<<<<
* ttype = VALID_HEADER_TYPES[record]
* data = new_header[record]
*/
- __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_v_new_header, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1354
+ /* "csamtools.pyx":1354
* for record in VALID_HEADERS:
* if record in new_header:
* ttype = VALID_HEADER_TYPES[record] # <<<<<<<<<<<<<<
__pyx_v_ttype = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":1355
+ /* "csamtools.pyx":1355
* if record in new_header:
* ttype = VALID_HEADER_TYPES[record]
* data = new_header[record] # <<<<<<<<<<<<<<
__pyx_v_data = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":1356
+ /* "csamtools.pyx":1356
* ttype = VALID_HEADER_TYPES[record]
* data = new_header[record]
* if type( data ) != type( ttype() ): # <<<<<<<<<<<<<<
*/
__pyx_t_6 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_6)), Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_6)), Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1357
+ /* "csamtools.pyx":1357
* data = new_header[record]
* if type( data ) != type( ttype() ):
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) ) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
}
__pyx_L6:;
- /* "pysam/csamtools.pyx":1358
+ /* "csamtools.pyx":1358
* if type( data ) != type( ttype() ):
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
* if type( data ) is dict: # <<<<<<<<<<<<<<
__pyx_t_5 = (((PyObject *)Py_TYPE(__pyx_v_data)) == ((PyObject *)((PyObject*)(&PyDict_Type))));
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1359
+ /* "csamtools.pyx":1359
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
* if type( data ) is dict:
* lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
* else:
* for fields in new_header[record]:
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
}
/*else*/ {
- /* "pysam/csamtools.pyx":1361
+ /* "csamtools.pyx":1361
* lines.append( self._buildLine( data, record ) )
* else:
* for fields in new_header[record]: # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_6)) {
+ if (PyList_CheckExact(__pyx_t_6)) {
if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_6)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_6)) {
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
+ } else if (PyTuple_CheckExact(__pyx_t_6)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
} else {
__pyx_t_7 = __pyx_t_10(__pyx_t_6);
if (unlikely(!__pyx_t_7)) {
__pyx_v_fields = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1362
+ /* "csamtools.pyx":1362
* else:
* for fields in new_header[record]:
* lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
*
* # then: user tags (lower case), sorted alphabetically
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1365
+ /* "csamtools.pyx":1365
*
* # then: user tags (lower case), sorted alphabetically
* for record, data in sorted(new_header.items()): # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
} else {
__pyx_t_6 = __pyx_t_4(__pyx_t_2);
if (unlikely(!__pyx_t_6)) {
}
if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
PyObject* sequence = __pyx_t_6;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_11 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_11 = PyList_GET_ITEM(sequence, 0);
__pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_11);
__Pyx_INCREF(__pyx_t_1);
- #else
- __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
index = 1; __pyx_t_1 = __pyx_t_12(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L13_unpacking_done;
__pyx_L12_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L13_unpacking_done:;
}
__pyx_v_data = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1366
+ /* "csamtools.pyx":1366
* # then: user tags (lower case), sorted alphabetically
* for record, data in sorted(new_header.items()):
* if record in VALID_HEADERS: continue # <<<<<<<<<<<<<<
*/
__pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_t_6, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = ((PySequence_Contains(__pyx_t_6, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_5) {
goto __pyx_L10_continue;
}
__pyx_L14:;
- /* "pysam/csamtools.pyx":1367
+ /* "csamtools.pyx":1367
* for record, data in sorted(new_header.items()):
* if record in VALID_HEADERS: continue
* if type( data ) is dict: # <<<<<<<<<<<<<<
__pyx_t_5 = (((PyObject *)Py_TYPE(__pyx_v_data)) == ((PyObject *)((PyObject*)(&PyDict_Type))));
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1368
+ /* "csamtools.pyx":1368
* if record in VALID_HEADERS: continue
* if type( data ) is dict:
* lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
* else:
* for fields in new_header[record]:
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
}
/*else*/ {
- /* "pysam/csamtools.pyx":1370
+ /* "csamtools.pyx":1370
* lines.append( self._buildLine( data, record ) )
* else:
* for fields in new_header[record]: # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_11 = PySequence_ITEM(__pyx_t_1, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_11 = PySequence_ITEM(__pyx_t_1, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
} else {
__pyx_t_11 = __pyx_t_10(__pyx_t_1);
if (unlikely(!__pyx_t_11)) {
__pyx_v_fields = __pyx_t_11;
__pyx_t_11 = 0;
- /* "pysam/csamtools.pyx":1371
+ /* "csamtools.pyx":1371
* else:
* for fields in new_header[record]:
* lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
*
* text = "\n".join(lines) + "\n"
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1373
+ /* "csamtools.pyx":1373
* lines.append( self._buildLine( fields, record ) )
*
* text = "\n".join(lines) + "\n" # <<<<<<<<<<<<<<
__pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_v_lines));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_lines));
__Pyx_GIVEREF(((PyObject *)__pyx_v_lines));
__pyx_v_text = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1374
+ /* "csamtools.pyx":1374
*
* text = "\n".join(lines) + "\n"
* if dest.text != NULL: free( dest.text ) # <<<<<<<<<<<<<<
}
__pyx_L18:;
- /* "pysam/csamtools.pyx":1375
+ /* "csamtools.pyx":1375
* text = "\n".join(lines) + "\n"
* if dest.text != NULL: free( dest.text )
* dest.text = <char*>calloc( len(text), sizeof(char)) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest->text = ((char *)calloc(__pyx_t_3, (sizeof(char))));
- /* "pysam/csamtools.pyx":1376
+ /* "csamtools.pyx":1376
* if dest.text != NULL: free( dest.text )
* dest.text = <char*>calloc( len(text), sizeof(char))
* dest.l_text = len(text) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest->l_text = __pyx_t_3;
- /* "pysam/csamtools.pyx":1377
+ /* "csamtools.pyx":1377
* dest.text = <char*>calloc( len(text), sizeof(char))
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<<
__pyx_v_btext = ((PyObject*)__pyx_t_7);
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1378
+ /* "csamtools.pyx":1378
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii')
* strncpy( dest.text, btext, dest.l_text ) # <<<<<<<<<<<<<<
__pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_btext)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
strncpy(__pyx_v_dest->text, __pyx_t_13, __pyx_v_dest->l_text);
- /* "pysam/csamtools.pyx":1382
+ /* "csamtools.pyx":1382
* cdef bytes bseqname
* # collect targets
* if "SQ" in new_header: # <<<<<<<<<<<<<<
* seqs = []
* for fields in new_header["SQ"]:
*/
- __pyx_t_5 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__SQ), __pyx_v_new_header, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1383
+ /* "csamtools.pyx":1383
* # collect targets
* if "SQ" in new_header:
* seqs = [] # <<<<<<<<<<<<<<
* try:
*/
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__pyx_v_seqs = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1384
+ /* "csamtools.pyx":1384
* if "SQ" in new_header:
* seqs = []
* for fields in new_header["SQ"]: # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else {
__pyx_t_7 = __pyx_t_4(__pyx_t_1);
if (unlikely(!__pyx_t_7)) {
__pyx_v_fields = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1385
+ /* "csamtools.pyx":1385
* seqs = []
* for fields in new_header["SQ"]:
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- /* "pysam/csamtools.pyx":1386
+ /* "csamtools.pyx":1386
* for fields in new_header["SQ"]:
* try:
* seqs.append( (fields["SN"], fields["LN"] ) ) # <<<<<<<<<<<<<<
* except KeyError:
* raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*/
+ if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ }
__pyx_t_7 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_2 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":1387
+ /* "csamtools.pyx":1387
* try:
* seqs.append( (fields["SN"], fields["LN"] ) )
* except KeyError: # <<<<<<<<<<<<<<
*/
__pyx_t_17 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_17) {
- __Pyx_AddTraceback("pysam.csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1387; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/csamtools.pyx":1388
+ /* "csamtools.pyx":1388
* seqs.append( (fields["SN"], fields["LN"] ) )
* except KeyError:
* raise KeyError( "incomplete sequence information in '%s'" % str(fields)) # <<<<<<<<<<<<<<
* dest.n_targets = len(seqs)
*/
__pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
__Pyx_GOTREF(((PyObject *)__pyx_t_11));
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
__pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
- __Pyx_GOTREF(__pyx_t_18);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_18));
PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11));
__Pyx_GIVEREF(((PyObject *)__pyx_t_11));
__pyx_t_11 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1390
+ /* "csamtools.pyx":1390
* raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*
* dest.n_targets = len(seqs) # <<<<<<<<<<<<<<
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*/
- __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs)); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs));
__pyx_v_dest->n_targets = __pyx_t_3;
- /* "pysam/csamtools.pyx":1391
+ /* "csamtools.pyx":1391
*
* dest.n_targets = len(seqs)
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) ) # <<<<<<<<<<<<<<
*/
__pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *))));
- /* "pysam/csamtools.pyx":1392
+ /* "csamtools.pyx":1392
* dest.n_targets = len(seqs)
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) ) # <<<<<<<<<<<<<<
*/
__pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t))));
- /* "pysam/csamtools.pyx":1394
+ /* "csamtools.pyx":1394
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*
* for x from 0 <= x < dest.n_targets: # <<<<<<<<<<<<<<
__pyx_t_19 = __pyx_v_dest->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_19; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":1395
+ /* "csamtools.pyx":1395
*
* for x from 0 <= x < dest.n_targets:
* seqname, seqlen = seqs[x] # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_1);
if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
PyObject* sequence = __pyx_t_1;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_7 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_7);
__Pyx_INCREF(__pyx_t_2);
- #else
- __pyx_t_7 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_6 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
index = 1; __pyx_t_2 = __pyx_t_12(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L34_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L35_unpacking_done;
__pyx_L34_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L35_unpacking_done:;
}
__pyx_v_seqlen = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1396
+ /* "csamtools.pyx":1396
* for x from 0 <= x < dest.n_targets:
* seqname, seqlen = seqs[x]
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) ) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
(__pyx_v_dest->target_name[__pyx_v_x]) = ((char *)calloc((__pyx_t_3 + 1), (sizeof(char))));
- /* "pysam/csamtools.pyx":1397
+ /* "csamtools.pyx":1397
* seqname, seqlen = seqs[x]
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<<
__pyx_v_bseqname = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1398
+ /* "csamtools.pyx":1398
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii')
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 ) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
strncpy((__pyx_v_dest->target_name[__pyx_v_x]), __pyx_t_13, (__pyx_t_3 + 1));
- /* "pysam/csamtools.pyx":1399
+ /* "csamtools.pyx":1399
* bseqname = seqname.encode('ascii')
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
* dest.target_len[x] = seqlen # <<<<<<<<<<<<<<
}
__pyx_L19:;
- /* "pysam/csamtools.pyx":1401
+ /* "csamtools.pyx":1401
* dest.target_len[x] = seqlen
*
* return dest # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_11);
__Pyx_XDECREF(__pyx_t_18);
- __Pyx_WriteUnraisable("pysam.csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_lines);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1411
+/* "csamtools.pyx":1411
* ## Possible solutions: deprecate or open new file handle
* ###############################################################
* def __iter__(self): # <<<<<<<<<<<<<<
* if not self.isbam and self.samfile.header.n_targets == 0:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1411);
- /* "pysam/csamtools.pyx":1412
+ /* "csamtools.pyx":1412
* ###############################################################
* def __iter__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header")
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1413
+ /* "csamtools.pyx":1413
* def __iter__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam and self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
* raise NotImplementedError( "can not iterate over samfile without header")
* return self
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
- __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
__pyx_t_5 = __pyx_t_3;
} else {
__pyx_t_5 = __pyx_t_4;
}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1414
+ /* "csamtools.pyx":1414
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1415
+ /* "csamtools.pyx":1415
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header")
* return self # <<<<<<<<<<<<<<
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1417
+/* "csamtools.pyx":1417
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
*
*/
-static bam1_t *__pyx_f_5pysam_9csamtools_7Samfile_getCurrent(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1417);
- /* "pysam/csamtools.pyx":1418
+ /* "csamtools.pyx":1418
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1420
+/* "csamtools.pyx":1420
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
* cversion of iterator. Used by :class:`pysam.Samfile.IteratorColumn`.
*/
-static int __pyx_f_5pysam_9csamtools_7Samfile_cnext(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1420);
- /* "pysam/csamtools.pyx":1425
+ /* "csamtools.pyx":1425
* '''
* cdef int ret
* return samread(self.samfile, self.b) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_7Samfile_42__next__[] = "\n python version of next().\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_42__next__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1427
+/* "csamtools.pyx":1427
* return samread(self.samfile, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
* python version of next().
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_42__next__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_21__next__[] = "\n python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_21__next__;
+static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1427);
- /* "pysam/csamtools.pyx":1432
+ /* "csamtools.pyx":1432
* """
* cdef int ret
* ret = samread(self.samfile, self.b) # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = samread(__pyx_v_self->samfile, __pyx_v_self->b);
+ __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1433
+ /* "csamtools.pyx":1433
* cdef int ret
* ret = samread(self.samfile, self.b)
* if (ret > 0): # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1434
+ /* "csamtools.pyx":1434
* ret = samread(self.samfile, self.b)
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1436
+ /* "csamtools.pyx":1436
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.Samfile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Samfile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1481
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+
+static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_tid;
int __pyx_v_beg;
int __pyx_v_end;
int __pyx_v_reopen;
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
__pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_v_beg = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_beg == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
if (values[4]) {
__pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
-
- /* "pysam/csamtools.pyx":1481
- * """
- *
- * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
__pyx_v_reopen = ((int)1);
}
}
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_beg, __pyx_v_end, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-static int __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- samfile_t *__pyx_t_6;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481);
-
- /* "pysam/csamtools.pyx":1483
+ /* "csamtools.pyx":1483
* def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1484
+ /* "csamtools.pyx":1484
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1486
+ /* "csamtools.pyx":1486
* raise ValueError( "I/O operation on closed file" )
*
* if not samfile._hasIndex(): # <<<<<<<<<<<<<<
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1487
+ /* "csamtools.pyx":1487
*
* if not samfile._hasIndex():
* raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":1491
+ /* "csamtools.pyx":1491
* # makes sure that samfile stays alive as long as the
* # iterator is alive
* self.samfile = samfile # <<<<<<<<<<<<<<
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile = __pyx_v_samfile;
- /* "pysam/csamtools.pyx":1493
+ /* "csamtools.pyx":1493
* self.samfile = samfile
*
* if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L5;
+ goto __pyx_L8;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1494
+ /* "csamtools.pyx":1494
*
* if samfile.isbam: mode = b"rb"
* else: mode = b"r" # <<<<<<<<<<<<<<
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L5:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":1498
+ /* "csamtools.pyx":1498
* # reopen the file - note that this makes the iterator
* # slow and causes pileup to slow down significantly.
* if reopen: # <<<<<<<<<<<<<<
*/
if (__pyx_v_reopen) {
- /* "pysam/csamtools.pyx":1499
+ /* "csamtools.pyx":1499
* # slow and causes pileup to slow down significantly.
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
__pyx_v_store = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1500
+ /* "csamtools.pyx":1500
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* assert self.fp != NULL
*/
__pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "pysam/csamtools.pyx":1501
+ /* "csamtools.pyx":1501
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1502
+ /* "csamtools.pyx":1502
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":1503
+ /* "csamtools.pyx":1503
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = self.samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L6;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L9;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1505
+ /* "csamtools.pyx":1505
* self.owns_samfile = True
* else:
* self.fp = self.samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- __pyx_t_6 = __pyx_v_self->samfile->samfile;
- __pyx_v_self->fp = __pyx_t_6;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->samfile;
- /* "pysam/csamtools.pyx":1506
+ /* "csamtools.pyx":1506
* else:
* self.fp = self.samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* self.retval = 0
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L6:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":1508
+ /* "csamtools.pyx":1508
* self.owns_samfile = False
*
* self.retval = 0 # <<<<<<<<<<<<<<
*
* self.iter = bam_iter_query(self.samfile.index,
*/
- __pyx_v_self->retval = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval = 0;
- /* "pysam/csamtools.pyx":1510
+ /* "csamtools.pyx":1510
* self.retval = 0
*
* self.iter = bam_iter_query(self.samfile.index, # <<<<<<<<<<<<<<
* tid,
* beg,
*/
- __pyx_v_self->iter = bam_iter_query(__pyx_v_self->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter = bam_iter_query(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
- /* "pysam/csamtools.pyx":1514
+ /* "csamtools.pyx":1514
* beg,
* end)
* self.b = bam_init1() # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- __pyx_v_self->b = bam_init1();
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b = bam_init1();
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1516
+/* "csamtools.pyx":1516
* self.b = bam_init1()
*
* def __iter__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1516);
- /* "pysam/csamtools.pyx":1517
+ /* "csamtools.pyx":1517
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1519
+/* "csamtools.pyx":1519
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
*
*/
-static bam1_t *__pyx_f_5pysam_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1519);
- /* "pysam/csamtools.pyx":1520
+ /* "csamtools.pyx":1520
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1522
+/* "csamtools.pyx":1522
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
* self.retval = bam_iter_read( self.fp.x.bam,
*/
-static int __pyx_f_5pysam_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1522);
- /* "pysam/csamtools.pyx":1524
+ /* "csamtools.pyx":1524
* cdef int cnext(self):
* '''cversion of iterator. Used by IteratorColumn'''
* self.retval = bam_iter_read( self.fp.x.bam, # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__[] = "python version of next().\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1528
+/* "csamtools.pyx":1528
* self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
* """
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_17IteratorRowRegion_2__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1528);
- /* "pysam/csamtools.pyx":1531
+ /* "csamtools.pyx":1531
* """python version of next().
* """
* self.cnext() # <<<<<<<<<<<<<<
* if self.retval < 0: raise StopIteration
* return makeAlignedRead( self.b )
*/
- ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
+ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
- /* "pysam/csamtools.pyx":1532
+ /* "csamtools.pyx":1532
* """
* self.cnext()
* if self.retval < 0: raise StopIteration # <<<<<<<<<<<<<<
* return makeAlignedRead( self.b )
*
*/
- __pyx_t_1 = (__pyx_v_self->retval < 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval < 0);
if (__pyx_t_1) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1533
+ /* "csamtools.pyx":1533
* self.cnext()
* if self.retval < 0: raise StopIteration
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
* def __dealloc__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":1535
+/* "csamtools.pyx":1535
* return makeAlignedRead( self.b )
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
* bam_iter_destroy( self.iter )
*/
-static void __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static void __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1535);
- /* "pysam/csamtools.pyx":1536
+ /* "csamtools.pyx":1536
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* bam_iter_destroy( self.iter )
* if self.owns_samfile: samclose( self.fp )
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1537
+ /* "csamtools.pyx":1537
* def __dealloc__(self):
* bam_destroy1(self.b)
* bam_iter_destroy( self.iter ) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_iter_destroy(__pyx_v_self->iter);
+ bam_iter_destroy(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter);
- /* "pysam/csamtools.pyx":1538
+ /* "csamtools.pyx":1538
* bam_destroy1(self.b)
* bam_iter_destroy( self.iter )
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* cdef class IteratorRowAll(IteratorRow):
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1550
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+
+static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_reopen;
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1550);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
if (values[1]) {
__pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
-
- /* "pysam/csamtools.pyx":1550
- * """
- *
- * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
__pyx_v_reopen = ((int)1);
}
}
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- samfile_t *__pyx_t_6;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1550);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":1552
+ /* "csamtools.pyx":1552
* def __cinit__(self, Samfile samfile, int reopen = True ):
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1553
+ /* "csamtools.pyx":1553
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1555
+ /* "csamtools.pyx":1555
* raise ValueError( "I/O operation on closed file" )
*
* if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L4;
+ goto __pyx_L7;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1556
+ /* "csamtools.pyx":1556
*
* if samfile.isbam: mode = b"rb"
* else: mode = b"r" # <<<<<<<<<<<<<<
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L4:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":1559
+ /* "csamtools.pyx":1559
*
* # reopen the file to avoid iterator conflict
* if reopen: # <<<<<<<<<<<<<<
*/
if (__pyx_v_reopen) {
- /* "pysam/csamtools.pyx":1560
+ /* "csamtools.pyx":1560
* # reopen the file to avoid iterator conflict
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
__pyx_v_store = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1561
+ /* "csamtools.pyx":1561
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* assert self.fp != NULL
*/
__pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "pysam/csamtools.pyx":1562
+ /* "csamtools.pyx":1562
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1563
+ /* "csamtools.pyx":1563
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":1564
+ /* "csamtools.pyx":1564
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L5;
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L8;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1566
+ /* "csamtools.pyx":1566
* self.owns_samfile = True
* else:
* self.fp = samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- __pyx_t_6 = __pyx_v_samfile->samfile;
- __pyx_v_self->fp = __pyx_t_6;
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
- /* "pysam/csamtools.pyx":1567
+ /* "csamtools.pyx":1567
* else:
* self.fp = samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* # allocate memory for alignment
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L5:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":1570
+ /* "csamtools.pyx":1570
*
* # allocate memory for alignment
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1572
+/* "csamtools.pyx":1572
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
* def __iter__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1572);
- /* "pysam/csamtools.pyx":1573
+ /* "csamtools.pyx":1573
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1575
+/* "csamtools.pyx":1575
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
*
*/
-static bam1_t *__pyx_f_5pysam_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
+static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1575);
- /* "pysam/csamtools.pyx":1576
+ /* "csamtools.pyx":1576
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1578
+/* "csamtools.pyx":1578
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
* return samread(self.fp, self.b)
*/
-static int __pyx_f_5pysam_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
+static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1578);
- /* "pysam/csamtools.pyx":1580
+ /* "csamtools.pyx":1580
* cdef int cnext(self):
* '''cversion of iterator. Used by IteratorColumn'''
* return samread(self.fp, self.b) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1582
+/* "csamtools.pyx":1582
* return samread(self.fp, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorRowAll_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1582);
- /* "pysam/csamtools.pyx":1588
+ /* "csamtools.pyx":1588
* """
* cdef int ret
* ret = samread(self.fp, self.b) # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_self->b);
+ __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp, ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1589
+ /* "csamtools.pyx":1589
* cdef int ret
* ret = samread(self.fp, self.b)
* if (ret > 0): # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1590
+ /* "csamtools.pyx":1590
* ret = samread(self.fp, self.b)
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1592
+ /* "csamtools.pyx":1592
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAll.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAll.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":1594
+/* "csamtools.pyx":1594
* raise StopIteration
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*/
-static void __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
+static void __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1594);
- /* "pysam/csamtools.pyx":1595
+ /* "csamtools.pyx":1595
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1596
+ /* "csamtools.pyx":1596
* def __dealloc__(self):
* bam_destroy1(self.b)
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* cdef class IteratorRowAllRefs(IteratorRow):
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1602
+ * """
+ *
+ * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ */
+
+static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1602);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self), __pyx_v_samfile);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1602
- * """
- *
- * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
- * assert samfile._isOpen()
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
- */
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-static int __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1602);
-
- /* "pysam/csamtools.pyx":1603
+ /* "csamtools.pyx":1603
*
* def __cinit__(self, Samfile samfile):
* assert samfile._isOpen() # <<<<<<<<<<<<<<
}
#endif
- /* "pysam/csamtools.pyx":1604
+ /* "csamtools.pyx":1604
* def __cinit__(self, Samfile samfile):
* assert samfile._isOpen()
* if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1605
+ /* "csamtools.pyx":1605
* assert samfile._isOpen()
* if not samfile._hasIndex(): raise ValueError("no index available for fetch")
* self.samfile = samfile # <<<<<<<<<<<<<<
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile = __pyx_v_samfile;
- /* "pysam/csamtools.pyx":1606
+ /* "csamtools.pyx":1606
* if not samfile._hasIndex(): raise ValueError("no index available for fetch")
* self.samfile = samfile
* self.tid = -1 # <<<<<<<<<<<<<<
*
* def nextiter(self):
*/
- __pyx_v_self->tid = -1;
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = -1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter[] = "IteratorRowAllRefs.nextiter(self)";
-static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("nextiter (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1608
+/* "csamtools.pyx":1608
* self.tid = -1
*
* def nextiter(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter[] = "IteratorRowAllRefs.nextiter(self)";
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("nextiter", 0);
+ __Pyx_RefNannySetupContext("nextiter");
__Pyx_TraceCall("nextiter", __pyx_f[0], 1608);
- /* "pysam/csamtools.pyx":1609
+ /* "csamtools.pyx":1609
*
* def nextiter(self):
* self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29) # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self->samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_int_536870912);
__Pyx_GIVEREF(__pyx_int_536870912);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(__pyx_v_self->rowiter);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->rowiter));
- __pyx_v_self->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_t_1);
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter));
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_1);
__pyx_t_1 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.nextiter", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.nextiter", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1611
+/* "csamtools.pyx":1611
* self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
*
* def __iter__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1611);
- /* "pysam/csamtools.pyx":1612
+ /* "csamtools.pyx":1612
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
* def __next__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1614
+/* "csamtools.pyx":1614
* return self
*
* def __next__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1614);
- /* "pysam/csamtools.pyx":1620
+ /* "csamtools.pyx":1620
* """
* # Create an initial iterator
* if self.tid==-1: # <<<<<<<<<<<<<<
* if not self.samfile.nreferences:
* raise StopIteration
*/
- __pyx_t_1 = (__pyx_v_self->tid == -1);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid == -1);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1621
+ /* "csamtools.pyx":1621
* # Create an initial iterator
* if self.tid==-1:
* if not self.samfile.nreferences: # <<<<<<<<<<<<<<
* raise StopIteration
* self.tid = 0
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = (!__pyx_t_1);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1622
+ /* "csamtools.pyx":1622
* if self.tid==-1:
* if not self.samfile.nreferences:
* raise StopIteration # <<<<<<<<<<<<<<
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1623
+ /* "csamtools.pyx":1623
* if not self.samfile.nreferences:
* raise StopIteration
* self.tid = 0 # <<<<<<<<<<<<<<
* self.nextiter()
*
*/
- __pyx_v_self->tid = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = 0;
- /* "pysam/csamtools.pyx":1624
+ /* "csamtools.pyx":1624
* raise StopIteration
* self.tid = 0
* self.nextiter() # <<<<<<<<<<<<<<
*
* while 1:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1626
+ /* "csamtools.pyx":1626
* self.nextiter()
*
* while 1: # <<<<<<<<<<<<<<
while (1) {
if (!1) break;
- /* "pysam/csamtools.pyx":1627
+ /* "csamtools.pyx":1627
*
* while 1:
* self.rowiter.cnext() # <<<<<<<<<<<<<<
*
* # If current iterator is not exhausted, return aligned read
*/
- ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self->rowiter->__pyx_vtab)->cnext(__pyx_v_self->rowiter);
+ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
- /* "pysam/csamtools.pyx":1630
+ /* "csamtools.pyx":1630
*
* # If current iterator is not exhausted, return aligned read
* if self.rowiter.retval>0: # <<<<<<<<<<<<<<
* return makeAlignedRead(self.rowiter.b)
*
*/
- __pyx_t_3 = (__pyx_v_self->rowiter->retval > 0);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->retval > 0);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1631
+ /* "csamtools.pyx":1631
* # If current iterator is not exhausted, return aligned read
* if self.rowiter.retval>0:
* return makeAlignedRead(self.rowiter.b) # <<<<<<<<<<<<<<
* self.tid += 1
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L7;
+ goto __pyx_L9;
}
- __pyx_L7:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":1633
+ /* "csamtools.pyx":1633
* return makeAlignedRead(self.rowiter.b)
*
* self.tid += 1 # <<<<<<<<<<<<<<
*
* # Otherwise, proceed to next reference or stop
*/
- __pyx_v_self->tid = (__pyx_v_self->tid + 1);
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid + 1);
- /* "pysam/csamtools.pyx":1636
+ /* "csamtools.pyx":1636
*
* # Otherwise, proceed to next reference or stop
* if self.tid<self.samfile.nreferences: # <<<<<<<<<<<<<<
* self.nextiter()
* else:
*/
- __pyx_t_4 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1637
+ /* "csamtools.pyx":1637
* # Otherwise, proceed to next reference or stop
* if self.tid<self.samfile.nreferences:
* self.nextiter() # <<<<<<<<<<<<<<
* else:
* raise StopIteration
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L8;
+ goto __pyx_L10;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1639
+ /* "csamtools.pyx":1639
* self.nextiter()
* else:
* raise StopIteration # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L8:;
+ __pyx_L10:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1647
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+
+static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
PyObject *__pyx_v_positions = 0;
int __pyx_v_reopen;
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__positions)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__positions);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
__pyx_v_positions = values[1];
if (values[2]) {
__pyx_v_reopen = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
-
- /* "pysam/csamtools.pyx":1647
- * """
- *
- * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
__pyx_v_reopen = ((int)1);
}
}
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self), __pyx_v_samfile, __pyx_v_positions, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- samfile_t *__pyx_t_6;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":1649
+ /* "csamtools.pyx":1649
* def __cinit__(self, Samfile samfile, positions, int reopen = True ):
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1650
+ /* "csamtools.pyx":1650
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1652
+ /* "csamtools.pyx":1652
* raise ValueError( "I/O operation on closed file" )
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1653
+ /* "csamtools.pyx":1653
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":1655
+ /* "csamtools.pyx":1655
* raise ValueError( "I/O operation on closed file" )
*
* assert samfile.isbam, "can only use this iterator on bam files" # <<<<<<<<<<<<<<
}
#endif
- /* "pysam/csamtools.pyx":1656
+ /* "csamtools.pyx":1656
*
* assert samfile.isbam, "can only use this iterator on bam files"
* mode = b"rb" # <<<<<<<<<<<<<<
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- /* "pysam/csamtools.pyx":1659
+ /* "csamtools.pyx":1659
*
* # reopen the file to avoid iterator conflict
* if reopen: # <<<<<<<<<<<<<<
*/
if (__pyx_v_reopen) {
- /* "pysam/csamtools.pyx":1660
+ /* "csamtools.pyx":1660
* # reopen the file to avoid iterator conflict
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
__pyx_v_store = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1661
+ /* "csamtools.pyx":1661
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* assert self.fp != NULL
*/
__pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "pysam/csamtools.pyx":1662
+ /* "csamtools.pyx":1662
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1663
+ /* "csamtools.pyx":1663
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":1664
+ /* "csamtools.pyx":1664
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L5;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L8;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1666
+ /* "csamtools.pyx":1666
* self.owns_samfile = True
* else:
* self.fp = samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- __pyx_t_6 = __pyx_v_samfile->samfile;
- __pyx_v_self->fp = __pyx_t_6;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
- /* "pysam/csamtools.pyx":1667
+ /* "csamtools.pyx":1667
* else:
* self.fp = samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* # allocate memory for alignment
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L5:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":1670
+ /* "csamtools.pyx":1670
*
* # allocate memory for alignment
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
* self.positions = positions
*/
- __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "pysam/csamtools.pyx":1672
+ /* "csamtools.pyx":1672
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
* self.positions = positions # <<<<<<<<<<<<<<
*/
__Pyx_INCREF(__pyx_v_positions);
__Pyx_GIVEREF(__pyx_v_positions);
- __Pyx_GOTREF(__pyx_v_self->positions);
- __Pyx_DECREF(__pyx_v_self->positions);
- __pyx_v_self->positions = __pyx_v_positions;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
+ __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions = __pyx_v_positions;
- /* "pysam/csamtools.pyx":1673
+ /* "csamtools.pyx":1673
*
* self.positions = positions
* self.current_pos = 0 # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- __pyx_v_self->current_pos = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->current_pos = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1675
+/* "csamtools.pyx":1675
* self.current_pos = 0
*
* def __iter__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1675);
- /* "pysam/csamtools.pyx":1676
+ /* "csamtools.pyx":1676
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1678
+/* "csamtools.pyx":1678
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
*
*/
-static bam1_t *__pyx_f_5pysam_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1678);
- /* "pysam/csamtools.pyx":1679
+ /* "csamtools.pyx":1679
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1681
+/* "csamtools.pyx":1681
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_f_5pysam_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1681);
- /* "pysam/csamtools.pyx":1685
+ /* "csamtools.pyx":1685
*
* # end iteration if out of positions
* if self.current_pos >= len(self.positions): return -1 # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1687
+ /* "csamtools.pyx":1687
* if self.current_pos >= len(self.positions): return -1
*
* bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
bam_seek(__pyx_v_self->fp->x.bam, __pyx_t_4, 0);
- /* "pysam/csamtools.pyx":1688
+ /* "csamtools.pyx":1688
*
* bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
* self.current_pos += 1 # <<<<<<<<<<<<<<
*/
__pyx_v_self->current_pos = (__pyx_v_self->current_pos + 1);
- /* "pysam/csamtools.pyx":1689
+ /* "csamtools.pyx":1689
* bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
* self.current_pos += 1
* return samread(self.fp, self.b) # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_WriteUnraisable("pysam.csamtools.IteratorRowSelection.cnext", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.IteratorRowSelection.cnext", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1691
+/* "csamtools.pyx":1691
* return samread(self.fp, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_20IteratorRowSelection_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1691);
- /* "pysam/csamtools.pyx":1697
+ /* "csamtools.pyx":1697
* """
*
* cdef int ret = self.cnext() # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
+ __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
- /* "pysam/csamtools.pyx":1698
+ /* "csamtools.pyx":1698
*
* cdef int ret = self.cnext()
* if (ret > 0): # <<<<<<<<<<<<<<
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1699
+ /* "csamtools.pyx":1699
* cdef int ret = self.cnext()
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1701
+ /* "csamtools.pyx":1701
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorRowSelection.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorRowSelection.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":1703
+/* "csamtools.pyx":1703
* raise StopIteration
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*/
-static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1703);
- /* "pysam/csamtools.pyx":1704
+ /* "csamtools.pyx":1704
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1705
+ /* "csamtools.pyx":1705
* def __dealloc__(self):
* bam_destroy1(self.b)
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* ##-------------------------------------------------------------------
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "pysam/csamtools.pyx":1710
+/* "csamtools.pyx":1710
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef int __advance_all( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
* '''
*/
-static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_5pysam_9csamtools___iterdata *__pyx_v_d;
+static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_9csamtools___iterdata *__pyx_v_d;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_all", 0);
+ __Pyx_RefNannySetupContext("__advance_all");
__Pyx_TraceCall("__advance_all", __pyx_f[0], 1710);
- /* "pysam/csamtools.pyx":1714
+ /* "csamtools.pyx":1714
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
*/
- __pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
- /* "pysam/csamtools.pyx":1715
+ /* "csamtools.pyx":1715
* cdef __iterdata * d
* d = <__iterdata*>data
* return bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1717
+/* "csamtools.pyx":1717
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
* the samtools pileup.
*/
-static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_5pysam_9csamtools___iterdata *__pyx_v_d;
+static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_9csamtools___iterdata *__pyx_v_d;
int __pyx_v_ret;
int __pyx_v_skip;
int __pyx_v_q;
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- int32_t __pyx_t_4;
+ PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- long __pyx_t_8;
+ long __pyx_t_7;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_snpcalls", 0);
+ __Pyx_RefNannySetupContext("__advance_snpcalls");
__Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1717);
- /* "pysam/csamtools.pyx":1722
+ /* "csamtools.pyx":1722
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*/
- __pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
- /* "pysam/csamtools.pyx":1724
+ /* "csamtools.pyx":1724
* d = <__iterdata*>data
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
*/
__pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
- /* "pysam/csamtools.pyx":1725
+ /* "csamtools.pyx":1725
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
* cdef int skip = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1727
+ /* "csamtools.pyx":1727
* cdef int skip = 0
* cdef int q
* cdef int is_cns = 1 # <<<<<<<<<<<<<<
*/
__pyx_v_is_cns = 1;
- /* "pysam/csamtools.pyx":1728
+ /* "csamtools.pyx":1728
* cdef int q
* cdef int is_cns = 1
* cdef int is_nobaq = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_is_nobaq = 0;
- /* "pysam/csamtools.pyx":1729
+ /* "csamtools.pyx":1729
* cdef int is_cns = 1
* cdef int is_nobaq = 0
* cdef int capQ_thres = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_capQ_thres = 0;
- /* "pysam/csamtools.pyx":1732
+ /* "csamtools.pyx":1732
*
* # reload sequence
* if d.fastafile != NULL and b.core.tid != d.tid: # <<<<<<<<<<<<<<
}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1733
+ /* "csamtools.pyx":1733
* # reload sequence
* if d.fastafile != NULL and b.core.tid != d.tid:
* if d.seq != NULL: free(d.seq) # <<<<<<<<<<<<<<
}
__pyx_L4:;
- /* "pysam/csamtools.pyx":1734
+ /* "csamtools.pyx":1734
* if d.fastafile != NULL and b.core.tid != d.tid:
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid # <<<<<<<<<<<<<<
* d.seq = faidx_fetch_seq(d.fastafile,
* d.samfile.header.target_name[d.tid],
*/
- __pyx_t_4 = __pyx_v_b->core.tid;
- __pyx_v_d->tid = __pyx_t_4;
+ __pyx_v_d->tid = __pyx_v_b->core.tid;
- /* "pysam/csamtools.pyx":1735
+ /* "csamtools.pyx":1735
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid
* d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<<
* d.samfile.header.target_name[d.tid],
* 0, max_pos,
*/
- __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_5pysam_9csamtools_max_pos, (&__pyx_v_d->seq_len));
+ __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_9csamtools_max_pos, (&__pyx_v_d->seq_len));
- /* "pysam/csamtools.pyx":1739
+ /* "csamtools.pyx":1739
* 0, max_pos,
* &d.seq_len)
* if d.seq == NULL: # <<<<<<<<<<<<<<
__pyx_t_3 = (__pyx_v_d->seq == NULL);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1741
+ /* "csamtools.pyx":1741
* if d.seq == NULL:
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
* (d.samfile.header.target_name[d.tid], # <<<<<<<<<<<<<<
* d.tid))
*
*/
- __pyx_t_5 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_4 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- /* "pysam/csamtools.pyx":1742
+ /* "csamtools.pyx":1742
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
* (d.samfile.header.target_name[d.tid],
* d.tid)) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_6 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_4 = 0;
__pyx_t_5 = 0;
- __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_126), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_126), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
}
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1745
+ /* "csamtools.pyx":1745
*
*
* while ret >= 0: # <<<<<<<<<<<<<<
__pyx_t_3 = (__pyx_v_ret >= 0);
if (!__pyx_t_3) break;
- /* "pysam/csamtools.pyx":1747
+ /* "csamtools.pyx":1747
* while ret >= 0:
*
* skip = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1750
+ /* "csamtools.pyx":1750
*
* # realign read - changes base qualities
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq ) # <<<<<<<<<<<<<<
}
__pyx_L8:;
- /* "pysam/csamtools.pyx":1752
+ /* "csamtools.pyx":1752
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq )
*
* if d.seq != NULL and capQ_thres > 10: # <<<<<<<<<<<<<<
}
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":1753
+ /* "csamtools.pyx":1753
*
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
*/
__pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
- /* "pysam/csamtools.pyx":1754
+ /* "csamtools.pyx":1754
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1 # <<<<<<<<<<<<<<
goto __pyx_L10;
}
- /* "pysam/csamtools.pyx":1755
+ /* "csamtools.pyx":1755
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q # <<<<<<<<<<<<<<
}
__pyx_L9:;
- /* "pysam/csamtools.pyx":1756
+ /* "csamtools.pyx":1756
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1 # <<<<<<<<<<<<<<
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*
*/
- __pyx_t_8 = (__pyx_v_b->core.flag & 4);
- if (__pyx_t_8) {
+ __pyx_t_7 = (__pyx_v_b->core.flag & 4);
+ if (__pyx_t_7) {
__pyx_v_skip = 1;
goto __pyx_L11;
}
- /* "pysam/csamtools.pyx":1757
+ /* "csamtools.pyx":1757
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 # <<<<<<<<<<<<<<
}
__pyx_L11:;
- /* "pysam/csamtools.pyx":1759
+ /* "csamtools.pyx":1759
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*
* if not skip: break # <<<<<<<<<<<<<<
}
__pyx_L12:;
- /* "pysam/csamtools.pyx":1762
+ /* "csamtools.pyx":1762
* # additional filters
*
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
}
__pyx_L7_break:;
- /* "pysam/csamtools.pyx":1764
+ /* "csamtools.pyx":1764
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* return ret # <<<<<<<<<<<<<<
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
- __Pyx_WriteUnraisable("pysam.csamtools.__advance_snpcalls", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("csamtools.__advance_snpcalls", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1813
+ * '''
+ *
+ * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ */
+
+static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1813);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1813
- * '''
- *
- * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
- */
-
-static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1813);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":1814
+ /* "csamtools.pyx":1814
*
* def __cinit__( self, Samfile samfile, **kwargs ):
* self.samfile = samfile # <<<<<<<<<<<<<<
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile = __pyx_v_samfile;
- /* "pysam/csamtools.pyx":1815
+ /* "csamtools.pyx":1815
* def __cinit__( self, Samfile samfile, **kwargs ):
* self.samfile = samfile
* self.mask = kwargs.get("mask", BAM_DEF_MASK ) # <<<<<<<<<<<<<<
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None )
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__mask), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_self->mask = __pyx_t_3;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->mask = __pyx_t_3;
- /* "pysam/csamtools.pyx":1816
+ /* "csamtools.pyx":1816
* self.samfile = samfile
* self.mask = kwargs.get("mask", BAM_DEF_MASK )
* self.fastafile = kwargs.get( "fastafile", None ) # <<<<<<<<<<<<<<
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 )
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__fastafile), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5pysam_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_v_self->fastafile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
- __pyx_v_self->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_t_2);
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1817
+ /* "csamtools.pyx":1817
* self.mask = kwargs.get("mask", BAM_DEF_MASK )
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None ) # <<<<<<<<<<<<<<
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__stepper), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_v_self->stepper);
- __Pyx_DECREF(__pyx_v_self->stepper);
- __pyx_v_self->stepper = __pyx_t_2;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
+ __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":1818
+ /* "csamtools.pyx":1818
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 ) # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
* self.tid = 0
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__max_depth), __pyx_int_8000); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_self->max_depth = __pyx_t_3;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->max_depth = __pyx_t_3;
- /* "pysam/csamtools.pyx":1819
+ /* "csamtools.pyx":1819
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
* self.tid = 0
* self.pos = 0
*/
- __pyx_v_self->iterdata.seq = NULL;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
- /* "pysam/csamtools.pyx":1820
+ /* "csamtools.pyx":1820
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL
* self.tid = 0 # <<<<<<<<<<<<<<
* self.pos = 0
* self.n_plp = 0
*/
- __pyx_v_self->tid = 0;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->tid = 0;
- /* "pysam/csamtools.pyx":1821
+ /* "csamtools.pyx":1821
* self.iterdata.seq = NULL
* self.tid = 0
* self.pos = 0 # <<<<<<<<<<<<<<
* self.n_plp = 0
* self.plp = NULL
*/
- __pyx_v_self->pos = 0;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pos = 0;
- /* "pysam/csamtools.pyx":1822
+ /* "csamtools.pyx":1822
* self.tid = 0
* self.pos = 0
* self.n_plp = 0 # <<<<<<<<<<<<<<
* self.plp = NULL
* self.pileup_iter = <bam_plp_t>NULL
*/
- __pyx_v_self->n_plp = 0;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->n_plp = 0;
- /* "pysam/csamtools.pyx":1823
+ /* "csamtools.pyx":1823
* self.pos = 0
* self.n_plp = 0
* self.plp = NULL # <<<<<<<<<<<<<<
* self.pileup_iter = <bam_plp_t>NULL
*
*/
- __pyx_v_self->plp = NULL;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->plp = NULL;
- /* "pysam/csamtools.pyx":1824
+ /* "csamtools.pyx":1824
* self.n_plp = 0
* self.plp = NULL
* self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
*
*
*/
- __pyx_v_self->pileup_iter = NULL;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1827
+/* "csamtools.pyx":1827
*
*
* def __iter__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1827);
- /* "pysam/csamtools.pyx":1828
+ /* "csamtools.pyx":1828
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
* cdef int cnext(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1830
+/* "csamtools.pyx":1830
* return self
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_f_5pysam_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
+static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1830);
- /* "pysam/csamtools.pyx":1836
+ /* "csamtools.pyx":1836
* It has been re-implemented to permit for filtering.
* '''
* self.plp = bam_plp_auto( self.pileup_iter, # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1841
+/* "csamtools.pyx":1841
* &self.n_plp )
*
* cdef char * getSequence( self ): # <<<<<<<<<<<<<<
* '''
*/
-static char *__pyx_f_5pysam_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
+static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getSequence", 0);
+ __Pyx_RefNannySetupContext("getSequence");
__Pyx_TraceCall("getSequence", __pyx_f[0], 1841);
- /* "pysam/csamtools.pyx":1844
+ /* "csamtools.pyx":1844
* '''return current reference sequence underlying the iterator.
* '''
* return self.iterdata.seq # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1848
+/* "csamtools.pyx":1848
* property seq_len:
* '''current sequence length.'''
* def __get__(self): return self.iterdata.seq_len # <<<<<<<<<<<<<<
* def addReference( self, Fastafile fastafile ):
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1848);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.seq_len.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.seq_len.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_14IteratorColumn_4addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("addReference (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_5pysam_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_fastafile));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1850
+/* "csamtools.pyx":1850
* def __get__(self): return self.iterdata.seq_len
*
* def addReference( self, Fastafile fastafile ): # <<<<<<<<<<<<<<
* add reference sequences in *fastafile* to iterator.'''
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_fastafile) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorColumn_2addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- faidx_t *__pyx_t_2;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("addReference", 0);
+ __Pyx_RefNannySetupContext("addReference");
__Pyx_TraceCall("addReference", __pyx_f[0], 1850);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":1853
+ /* "csamtools.pyx":1853
* '''
* add reference sequences in *fastafile* to iterator.'''
* self.fastafile = fastafile # <<<<<<<<<<<<<<
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_fastafile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_fastafile));
- __Pyx_GOTREF(__pyx_v_self->fastafile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
- __pyx_v_self->fastafile = __pyx_v_fastafile;
+ __Pyx_INCREF(__pyx_v_fastafile);
+ __Pyx_GIVEREF(__pyx_v_fastafile);
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_fastafile);
- /* "pysam/csamtools.pyx":1854
+ /* "csamtools.pyx":1854
* add reference sequences in *fastafile* to iterator.'''
* self.fastafile = fastafile
* if self.iterdata.seq != NULL: free(self.iterdata.seq) # <<<<<<<<<<<<<<
* self.iterdata.tid = -1
* self.iterdata.fastafile = self.fastafile.fastafile
*/
- __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
if (__pyx_t_1) {
- free(__pyx_v_self->iterdata.seq);
- goto __pyx_L3;
+ free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1855
+ /* "csamtools.pyx":1855
* self.fastafile = fastafile
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
* self.iterdata.fastafile = self.fastafile.fastafile
*
*/
- __pyx_v_self->iterdata.tid = -1;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.tid = -1;
- /* "pysam/csamtools.pyx":1856
+ /* "csamtools.pyx":1856
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1
* self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
*
* def hasReference( self ):
*/
- __pyx_t_2 = __pyx_v_self->fastafile->fastafile;
- __pyx_v_self->iterdata.fastafile = __pyx_t_2;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.fastafile = ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile->fastafile;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.IteratorColumn.addReference", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_14IteratorColumn_6hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
-static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("hasReference (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1858
+/* "csamtools.pyx":1858
* self.iterdata.fastafile = self.fastafile.fastafile
*
* def hasReference( self ): # <<<<<<<<<<<<<<
* return true if iterator is associated with a reference'''
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorColumn_3hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("hasReference", 0);
+ __Pyx_RefNannySetupContext("hasReference");
__Pyx_TraceCall("hasReference", __pyx_f[0], 1858);
- /* "pysam/csamtools.pyx":1861
+ /* "csamtools.pyx":1861
* '''
* return true if iterator is associated with a reference'''
* return self.fastafile # <<<<<<<<<<<<<<
* cdef setMask( self, mask ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->fastafile));
- __pyx_r = ((PyObject *)__pyx_v_self->fastafile);
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
+ __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1863
+/* "csamtools.pyx":1863
* return self.fastafile
*
* cdef setMask( self, mask ): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_f_5pysam_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_mask) {
+static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_mask) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setMask", 0);
+ __Pyx_RefNannySetupContext("setMask");
__Pyx_TraceCall("setMask", __pyx_f[0], 1863);
- /* "pysam/csamtools.pyx":1868
+ /* "csamtools.pyx":1868
* reads with bits set in *mask* will be skipped.
* '''
* self.mask = mask # <<<<<<<<<<<<<<
__pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_mask); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_self->mask = __pyx_t_1;
- /* "pysam/csamtools.pyx":1869
+ /* "csamtools.pyx":1869
* '''
* self.mask = mask
* bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.setMask", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.setMask", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1871
+/* "csamtools.pyx":1871
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
* int start,
*/
-static PyObject *__pyx_f_5pysam_9csamtools_14IteratorColumn_setupIteratorData(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args) {
+static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args) {
int __pyx_v_reopen = ((int)0);
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
- samfile_t *__pyx_t_6;
- bam_iter_t __pyx_t_7;
+ int __pyx_t_6;
+ int __pyx_t_7;
int __pyx_t_8;
- faidx_t *__pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setupIteratorData", 0);
+ __Pyx_RefNannySetupContext("setupIteratorData");
__Pyx_TraceCall("setupIteratorData", __pyx_f[0], 1871);
if (__pyx_optional_args) {
if (__pyx_optional_args->__pyx_n > 0) {
}
}
- /* "pysam/csamtools.pyx":1878
+ /* "csamtools.pyx":1878
* '''setup the iterator structure'''
*
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen ) # <<<<<<<<<<<<<<
__pyx_t_4 = PyInt_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
__pyx_t_2 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_GIVEREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_v_self->iter);
__Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
- __pyx_v_self->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_t_4);
+ __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":1879
+ /* "csamtools.pyx":1879
*
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
* self.iterdata.samfile = self.samfile.samfile # <<<<<<<<<<<<<<
* self.iterdata.iter = self.iter.iter
* self.iterdata.seq = NULL
*/
- __pyx_t_6 = __pyx_v_self->samfile->samfile;
- __pyx_v_self->iterdata.samfile = __pyx_t_6;
+ __pyx_v_self->iterdata.samfile = __pyx_v_self->samfile->samfile;
- /* "pysam/csamtools.pyx":1880
+ /* "csamtools.pyx":1880
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
* self.iterdata.samfile = self.samfile.samfile
* self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
* self.iterdata.tid = -1
*/
- __pyx_t_7 = __pyx_v_self->iter->iter;
- __pyx_v_self->iterdata.iter = __pyx_t_7;
+ __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
- /* "pysam/csamtools.pyx":1881
+ /* "csamtools.pyx":1881
* self.iterdata.samfile = self.samfile.samfile
* self.iterdata.iter = self.iter.iter
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_self->iterdata.seq = NULL;
- /* "pysam/csamtools.pyx":1882
+ /* "csamtools.pyx":1882
* self.iterdata.iter = self.iter.iter
* self.iterdata.seq = NULL
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
*/
__pyx_v_self->iterdata.tid = -1;
- /* "pysam/csamtools.pyx":1884
+ /* "csamtools.pyx":1884
* self.iterdata.tid = -1
*
* if self.fastafile != None: # <<<<<<<<<<<<<<
* self.iterdata.fastafile = self.fastafile.fastafile
* else:
*/
- __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_self->fastafile), Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_self->fastafile), Py_None, Py_NE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_8) {
+ if (__pyx_t_6) {
- /* "pysam/csamtools.pyx":1885
+ /* "csamtools.pyx":1885
*
* if self.fastafile != None:
* self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
* else:
* self.iterdata.fastafile = NULL
*/
- __pyx_t_9 = __pyx_v_self->fastafile->fastafile;
- __pyx_v_self->iterdata.fastafile = __pyx_t_9;
+ __pyx_v_self->iterdata.fastafile = __pyx_v_self->fastafile->fastafile;
goto __pyx_L3;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1887
+ /* "csamtools.pyx":1887
* self.iterdata.fastafile = self.fastafile.fastafile
* else:
* self.iterdata.fastafile = NULL # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1889
+ /* "csamtools.pyx":1889
* self.iterdata.fastafile = NULL
*
* if self.stepper == None or self.stepper == "all": # <<<<<<<<<<<<<<
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
* elif self.stepper == "samtools":
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, Py_None, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!__pyx_t_8) {
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_11 = __pyx_t_10;
+ if (!__pyx_t_6) {
+ __pyx_t_7 = __Pyx_PyString_Equals(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __pyx_t_7;
} else {
- __pyx_t_11 = __pyx_t_8;
+ __pyx_t_8 = __pyx_t_6;
}
- if (__pyx_t_11) {
+ if (__pyx_t_8) {
- /* "pysam/csamtools.pyx":1890
+ /* "csamtools.pyx":1890
*
* if self.stepper == None or self.stepper == "all":
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata ) # <<<<<<<<<<<<<<
* elif self.stepper == "samtools":
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
*/
- __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_5pysam_9csamtools___advance_all), (&__pyx_v_self->iterdata));
+ __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_all), (&__pyx_v_self->iterdata));
goto __pyx_L4;
}
- /* "pysam/csamtools.pyx":1891
+ /* "csamtools.pyx":1891
* if self.stepper == None or self.stepper == "all":
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
* elif self.stepper == "samtools": # <<<<<<<<<<<<<<
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
* else:
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__samtools), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_11) {
+ __pyx_t_8 = __Pyx_PyString_Equals(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__samtools), Py_EQ); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_8) {
- /* "pysam/csamtools.pyx":1892
+ /* "csamtools.pyx":1892
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
* elif self.stepper == "samtools":
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata ) # <<<<<<<<<<<<<<
* else:
* raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
*/
- __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_5pysam_9csamtools___advance_snpcalls), (&__pyx_v_self->iterdata));
+ __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_snpcalls), (&__pyx_v_self->iterdata));
goto __pyx_L4;
}
/*else*/ {
- /* "pysam/csamtools.pyx":1894
+ /* "csamtools.pyx":1894
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
* else:
* raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) # <<<<<<<<<<<<<<
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_127), __pyx_v_self->stepper); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
}
__pyx_L4:;
- /* "pysam/csamtools.pyx":1896
+ /* "csamtools.pyx":1896
* raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
*
* if self.max_depth: # <<<<<<<<<<<<<<
*/
if (__pyx_v_self->max_depth) {
- /* "pysam/csamtools.pyx":1897
+ /* "csamtools.pyx":1897
*
* if self.max_depth:
* bam_plp_set_maxcnt( self.pileup_iter, self.max_depth ) # <<<<<<<<<<<<<<
}
__pyx_L5:;
- /* "pysam/csamtools.pyx":1899
+ /* "csamtools.pyx":1899
* bam_plp_set_maxcnt( self.pileup_iter, self.max_depth )
*
* bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.setupIteratorData", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.setupIteratorData", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1901
+/* "csamtools.pyx":1901
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
* cdef reset( self, tid, start, end ): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_f_5pysam_9csamtools_14IteratorColumn_reset(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_end) {
+static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_end) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- bam_iter_t __pyx_t_4;
- int __pyx_t_5;
+ int __pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_RefNannySetupContext("reset");
__Pyx_TraceCall("reset", __pyx_f[0], 1901);
- /* "pysam/csamtools.pyx":1907
+ /* "csamtools.pyx":1907
* having to incur the full set-up costs.
* '''
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 ) # <<<<<<<<<<<<<<
*
*/
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_GIVEREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_v_self->iter);
__Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
- __pyx_v_self->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_t_3);
+ __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":1908
+ /* "csamtools.pyx":1908
* '''
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 )
* self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
*
* # invalidate sequence if different tid
*/
- __pyx_t_4 = __pyx_v_self->iter->iter;
- __pyx_v_self->iterdata.iter = __pyx_t_4;
+ __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
- /* "pysam/csamtools.pyx":1911
+ /* "csamtools.pyx":1911
*
* # invalidate sequence if different tid
* if self.tid != tid: # <<<<<<<<<<<<<<
*/
__pyx_t_3 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_v_tid, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_v_tid, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_5) {
+ if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1912
+ /* "csamtools.pyx":1912
* # invalidate sequence if different tid
* if self.tid != tid:
* if self.iterdata.seq != NULL: free( self.iterdata.seq ) # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
* self.iterdata.tid = -1
*/
- __pyx_t_5 = (__pyx_v_self->iterdata.seq != NULL);
- if (__pyx_t_5) {
+ __pyx_t_4 = (__pyx_v_self->iterdata.seq != NULL);
+ if (__pyx_t_4) {
free(__pyx_v_self->iterdata.seq);
goto __pyx_L4;
}
__pyx_L4:;
- /* "pysam/csamtools.pyx":1913
+ /* "csamtools.pyx":1913
* if self.tid != tid:
* if self.iterdata.seq != NULL: free( self.iterdata.seq )
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
*/
__pyx_v_self->iterdata.seq = NULL;
- /* "pysam/csamtools.pyx":1914
+ /* "csamtools.pyx":1914
* if self.iterdata.seq != NULL: free( self.iterdata.seq )
* self.iterdata.seq = NULL
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1917
+ /* "csamtools.pyx":1917
*
* # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata )
* bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumn.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":1919
+/* "csamtools.pyx":1919
* bam_plp_reset(self.pileup_iter)
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
* # not been fully consumed
*/
-static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
+static void __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1919);
- /* "pysam/csamtools.pyx":1922
+ /* "csamtools.pyx":1922
* # reset in order to avoid memory leak messages for iterators that have
* # not been fully consumed
* if self.pileup_iter != <bam_plp_t>NULL: # <<<<<<<<<<<<<<
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter)
*/
- __pyx_t_1 = (__pyx_v_self->pileup_iter != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter != ((bam_plp_t)NULL));
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1923
+ /* "csamtools.pyx":1923
* # not been fully consumed
* if self.pileup_iter != <bam_plp_t>NULL:
* bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
* bam_plp_destroy(self.pileup_iter)
* self.pileup_iter = <bam_plp_t>NULL
*/
- bam_plp_reset(__pyx_v_self->pileup_iter);
+ bam_plp_reset(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
- /* "pysam/csamtools.pyx":1924
+ /* "csamtools.pyx":1924
* if self.pileup_iter != <bam_plp_t>NULL:
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter) # <<<<<<<<<<<<<<
* self.pileup_iter = <bam_plp_t>NULL
*
*/
- bam_plp_destroy(__pyx_v_self->pileup_iter);
+ bam_plp_destroy(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
- /* "pysam/csamtools.pyx":1925
+ /* "csamtools.pyx":1925
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter)
* self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
*
* if self.iterdata.seq != NULL:
*/
- __pyx_v_self->pileup_iter = NULL;
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":1927
+ /* "csamtools.pyx":1927
* self.pileup_iter = <bam_plp_t>NULL
*
* if self.iterdata.seq != NULL: # <<<<<<<<<<<<<<
* free(self.iterdata.seq)
* self.iterdata.seq = NULL
*/
- __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1928
+ /* "csamtools.pyx":1928
*
* if self.iterdata.seq != NULL:
* free(self.iterdata.seq) # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
*
*/
- free(__pyx_v_self->iterdata.seq);
+ free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
- /* "pysam/csamtools.pyx":1929
+ /* "csamtools.pyx":1929
* if self.iterdata.seq != NULL:
* free(self.iterdata.seq)
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
*
* cdef class IteratorColumnRegion(IteratorColumn):
*/
- __pyx_v_self->iterdata.seq = NULL;
- goto __pyx_L4;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1934
+ * '''iterates over a region only.
+ * '''
+ * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
+ * int tid = 0,
+ * int start = 0,
+ */
+
+static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_tid;
int __pyx_v_start;
int __pyx_v_end;
int __pyx_v_truncate;
- CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1934);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
if (values[1]) {
__pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1935; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
- /* "pysam/csamtools.pyx":1938
+ /* "csamtools.pyx":1938
* int start = 0,
* int end = max_pos,
* int truncate = False, # <<<<<<<<<<<<<<
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_truncate, __pyx_v_kwargs);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1934
- * '''iterates over a region only.
- * '''
- * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
- * int tid = 0,
- * int start = 0,
- */
-
-static int __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1934);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":1942
+ /* "csamtools.pyx":1942
*
* # initialize iterator
* self.setupIteratorData( tid, start, end, 1 ) # <<<<<<<<<<<<<<
*/
__pyx_t_2.__pyx_n = 1;
__pyx_t_2.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1943
+ /* "csamtools.pyx":1943
* # initialize iterator
* self.setupIteratorData( tid, start, end, 1 )
* self.start = start # <<<<<<<<<<<<<<
* self.end = end
* self.truncate = truncate
*/
- __pyx_v_self->start = __pyx_v_start;
+ ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start = __pyx_v_start;
- /* "pysam/csamtools.pyx":1944
+ /* "csamtools.pyx":1944
* self.setupIteratorData( tid, start, end, 1 )
* self.start = start
* self.end = end # <<<<<<<<<<<<<<
* self.truncate = truncate
*
*/
- __pyx_v_self->end = __pyx_v_end;
+ ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end = __pyx_v_end;
- /* "pysam/csamtools.pyx":1945
+ /* "csamtools.pyx":1945
* self.start = start
* self.end = end
* self.truncate = truncate # <<<<<<<<<<<<<<
*
* def __next__(self):
*/
- __pyx_v_self->truncate = __pyx_v_truncate;
+ ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate = __pyx_v_truncate;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__[] = "python version of next().\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1947
+/* "csamtools.pyx":1947
* self.truncate = truncate
*
* def __next__(self): # <<<<<<<<<<<<<<
* """
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
+static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1947);
- /* "pysam/csamtools.pyx":1951
+ /* "csamtools.pyx":1951
* """
*
* while 1: # <<<<<<<<<<<<<<
while (1) {
if (!1) break;
- /* "pysam/csamtools.pyx":1952
+ /* "csamtools.pyx":1952
*
* while 1:
* self.cnext() # <<<<<<<<<<<<<<
* if self.n_plp < 0:
* raise ValueError("error during iteration" )
*/
- ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- /* "pysam/csamtools.pyx":1953
+ /* "csamtools.pyx":1953
* while 1:
* self.cnext()
* if self.n_plp < 0: # <<<<<<<<<<<<<<
* raise ValueError("error during iteration" )
*
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1954
+ /* "csamtools.pyx":1954
* self.cnext()
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":1956
+ /* "csamtools.pyx":1956
* raise ValueError("error during iteration" )
*
* if self.plp == NULL: # <<<<<<<<<<<<<<
* raise StopIteration
*
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.plp == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp == NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1957
+ /* "csamtools.pyx":1957
*
* if self.plp == NULL:
* raise StopIteration # <<<<<<<<<<<<<<
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":1959
+ /* "csamtools.pyx":1959
* raise StopIteration
*
* if self.truncate: # <<<<<<<<<<<<<<
* if self.start < self.pos: continue
* if self.pos >= self.end: raise StopIteration
*/
- if (__pyx_v_self->truncate) {
+ if (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate) {
- /* "pysam/csamtools.pyx":1960
+ /* "csamtools.pyx":1960
*
* if self.truncate:
* if self.start < self.pos: continue # <<<<<<<<<<<<<<
* if self.pos >= self.end: raise StopIteration
*
*/
- __pyx_t_1 = (__pyx_v_self->start < __pyx_v_self->__pyx_base.pos);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start < ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos);
if (__pyx_t_1) {
- goto __pyx_L3_continue;
- goto __pyx_L8;
+ goto __pyx_L5_continue;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":1961
+ /* "csamtools.pyx":1961
* if self.truncate:
* if self.start < self.pos: continue
* if self.pos >= self.end: raise StopIteration # <<<<<<<<<<<<<<
*
* return makePileupProxy( &self.plp,
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.pos >= __pyx_v_self->end);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos >= ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end);
if (__pyx_t_1) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
+ goto __pyx_L11;
}
- __pyx_L9:;
- goto __pyx_L7;
+ __pyx_L11:;
+ goto __pyx_L9;
}
- __pyx_L7:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":1963
+ /* "csamtools.pyx":1963
* if self.pos >= self.end: raise StopIteration
*
* return makePileupProxy( &self.plp, # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
- /* "pysam/csamtools.pyx":1966
+ /* "csamtools.pyx":1966
* self.tid,
* self.pos,
* self.n_plp ) # <<<<<<<<<<<<<<
*
* cdef class IteratorColumnAllRefs(IteratorColumn):
*/
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- __pyx_L3_continue:;
+ __pyx_L5_continue:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
- CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
+/* "csamtools.pyx":1972
+ * """
+ *
+ * def __cinit__(self, # <<<<<<<<<<<<<<
+ * Samfile samfile,
+ * **kwargs ):
+ */
+
+static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1972);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-/* "pysam/csamtools.pyx":1972
- * """
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * Samfile samfile,
- * **kwargs ):
- */
-
-static int __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- int __pyx_t_3;
- struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1972);
-
- /* "pysam/csamtools.pyx":1977
+ /* "csamtools.pyx":1977
*
* # no iteration over empty files
* if not samfile.nreferences: raise StopIteration # <<<<<<<<<<<<<<
if (__pyx_t_3) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":1980
+ /* "csamtools.pyx":1980
*
* # initialize iterator
* self.setupIteratorData( self.tid, 0, max_pos, 1 ) # <<<<<<<<<<<<<<
*/
__pyx_t_4.__pyx_n = 1;
__pyx_t_4.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_5pysam_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__[] = "python version of next().\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":1982
+/* "csamtools.pyx":1982
* self.setupIteratorData( self.tid, 0, max_pos, 1 )
*
* def __next__(self): # <<<<<<<<<<<<<<
* """
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
+static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_5;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_5;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1982);
- /* "pysam/csamtools.pyx":1986
+ /* "csamtools.pyx":1986
* """
*
* while 1: # <<<<<<<<<<<<<<
while (1) {
if (!1) break;
- /* "pysam/csamtools.pyx":1987
+ /* "csamtools.pyx":1987
*
* while 1:
* self.cnext() # <<<<<<<<<<<<<<
*
* if self.n_plp < 0:
*/
- ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- /* "pysam/csamtools.pyx":1989
+ /* "csamtools.pyx":1989
* self.cnext()
*
* if self.n_plp < 0: # <<<<<<<<<<<<<<
* raise ValueError("error during iteration" )
*
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1990
+ /* "csamtools.pyx":1990
*
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":1993
+ /* "csamtools.pyx":1993
*
* # return result, if within same reference
* if self.plp != NULL: # <<<<<<<<<<<<<<
* return makePileupProxy( &self.plp,
* self.tid,
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1994
+ /* "csamtools.pyx":1994
* # return result, if within same reference
* if self.plp != NULL:
* return makePileupProxy( &self.plp, # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
- /* "pysam/csamtools.pyx":1997
+ /* "csamtools.pyx":1997
* self.tid,
* self.pos,
* self.n_plp ) # <<<<<<<<<<<<<<
*
* # otherwise, proceed to next reference or stop
*/
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":2000
+ /* "csamtools.pyx":2000
*
* # otherwise, proceed to next reference or stop
* self.tid += 1 # <<<<<<<<<<<<<<
* if self.tid < self.samfile.nreferences:
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
*/
- __pyx_v_self->__pyx_base.tid = (__pyx_v_self->__pyx_base.tid + 1);
+ ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid + 1);
- /* "pysam/csamtools.pyx":2001
+ /* "csamtools.pyx":2001
* # otherwise, proceed to next reference or stop
* self.tid += 1
* if self.tid < self.samfile.nreferences: # <<<<<<<<<<<<<<
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
* else:
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_self->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2002
+ /* "csamtools.pyx":2002
* self.tid += 1
* if self.tid < self.samfile.nreferences:
* self.setupIteratorData( self.tid, 0, max_pos, 0 ) # <<<<<<<<<<<<<<
*/
__pyx_t_5.__pyx_n = 1;
__pyx_t_5.reopen = 0;
- __pyx_t_4 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_5pysam_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L7;
+ goto __pyx_L9;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2004
+ /* "csamtools.pyx":2004
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L7:;
+ __pyx_L9:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2009
+/* "csamtools.pyx":2009
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_start(bam1_t *src) except -1: # <<<<<<<<<<<<<<
* cdef uint32_t k
*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx_v_src) {
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) {
uint32_t *__pyx_v_cigar_p;
uint32_t __pyx_v_op;
uint32_t __pyx_v_k;
int __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_start", 0);
+ __Pyx_RefNannySetupContext("query_start");
__Pyx_TraceCall("query_start", __pyx_f[0], 2009);
- /* "pysam/csamtools.pyx":2012
+ /* "csamtools.pyx":2012
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
* cdef uint32_t start_offset = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_start_offset = 0;
- /* "pysam/csamtools.pyx":2014
+ /* "csamtools.pyx":2014
* cdef uint32_t start_offset = 0
*
* if src.core.n_cigar: # <<<<<<<<<<<<<<
*/
if (__pyx_v_src->core.n_cigar) {
- /* "pysam/csamtools.pyx":2015
+ /* "csamtools.pyx":2015
*
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2016
+ /* "csamtools.pyx":2016
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
__pyx_t_1 = __pyx_v_src->core.n_cigar;
for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2017
+ /* "csamtools.pyx":2017
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2022
+ /* "csamtools.pyx":2022
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2018
+ /* "csamtools.pyx":2018
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
*/
case 5:
- /* "pysam/csamtools.pyx":2019
+ /* "csamtools.pyx":2019
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2020
+ /* "csamtools.pyx":2020
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
PyErr_SetString(__pyx_t_5, __pyx_k_132);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":2021
+ /* "csamtools.pyx":2021
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2022
+ /* "csamtools.pyx":2022
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
*/
case 4:
- /* "pysam/csamtools.pyx":2023
+ /* "csamtools.pyx":2023
* return -1
* elif op==BAM_CSOFT_CLIP:
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
break;
default:
- /* "pysam/csamtools.pyx":2025
+ /* "csamtools.pyx":2025
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2027
+ /* "csamtools.pyx":2027
* break
*
* return start_offset # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2032
+/* "csamtools.pyx":2032
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
* cdef uint32_t k
*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v_src) {
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
uint32_t *__pyx_v_cigar_p;
uint32_t __pyx_v_op;
uint32_t __pyx_v_k;
uint32_t __pyx_v_end_offset;
int32_t __pyx_r;
__Pyx_RefNannyDeclarations
- int32_t __pyx_t_1;
+ int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_4 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_end", 0);
+ __Pyx_RefNannySetupContext("query_end");
__Pyx_TraceCall("query_end", __pyx_f[0], 2032);
- /* "pysam/csamtools.pyx":2035
+ /* "csamtools.pyx":2035
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
* cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
* if src.core.n_cigar>1:
*/
- __pyx_t_1 = __pyx_v_src->core.l_qseq;
- __pyx_v_end_offset = __pyx_t_1;
+ __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
- /* "pysam/csamtools.pyx":2037
+ /* "csamtools.pyx":2037
* cdef uint32_t end_offset = src.core.l_qseq
*
* if src.core.n_cigar>1: # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar > 1);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar > 1);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2038
+ /* "csamtools.pyx":2038
*
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2039
+ /* "csamtools.pyx":2039
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<<
*/
for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
- /* "pysam/csamtools.pyx":2040
+ /* "csamtools.pyx":2040
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2045
+ /* "csamtools.pyx":2045
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2041
+ /* "csamtools.pyx":2041
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
*/
case 5:
- /* "pysam/csamtools.pyx":2042
+ /* "csamtools.pyx":2042
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
*/
- __pyx_t_2 = (__pyx_v_end_offset != 0);
- if (__pyx_t_2) {
- __pyx_t_3 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
- __pyx_t_4 = __pyx_t_3;
+ __pyx_t_1 = (__pyx_v_end_offset != 0);
+ if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
+ __pyx_t_3 = __pyx_t_2;
} else {
- __pyx_t_4 = __pyx_t_2;
+ __pyx_t_3 = __pyx_t_1;
}
- if (__pyx_t_4) {
+ if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":2043
+ /* "csamtools.pyx":2043
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
* return -1
* elif op==BAM_CSOFT_CLIP:
*/
- __pyx_t_5 = __pyx_builtin_ValueError;
- __Pyx_INCREF(__pyx_t_5);
- PyErr_SetString(__pyx_t_5, __pyx_k_132);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __pyx_builtin_ValueError;
+ __Pyx_INCREF(__pyx_t_4);
+ PyErr_SetString(__pyx_t_4, __pyx_k_132);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":2044
+ /* "csamtools.pyx":2044
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2045
+ /* "csamtools.pyx":2045
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
*/
case 4:
- /* "pysam/csamtools.pyx":2046
+ /* "csamtools.pyx":2046
* return -1
* elif op==BAM_CSOFT_CLIP:
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
break;
default:
- /* "pysam/csamtools.pyx":2048
+ /* "csamtools.pyx":2048
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2050
+ /* "csamtools.pyx":2050
* break
*
* if end_offset==0: # <<<<<<<<<<<<<<
* end_offset = src.core.l_qseq
*
*/
- __pyx_t_4 = (__pyx_v_end_offset == 0);
- if (__pyx_t_4) {
+ __pyx_t_3 = (__pyx_v_end_offset == 0);
+ if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":2051
+ /* "csamtools.pyx":2051
*
* if end_offset==0:
* end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
* return end_offset
*/
- __pyx_t_1 = __pyx_v_src->core.l_qseq;
- __pyx_v_end_offset = __pyx_t_1;
+ __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
goto __pyx_L7;
}
__pyx_L7:;
- /* "pysam/csamtools.pyx":2053
+ /* "csamtools.pyx":2053
* end_offset = src.core.l_qseq
*
* return end_offset # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2056
+/* "csamtools.pyx":2056
*
*
* cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
* cdef uint32_t k
*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
uint8_t *__pyx_v_p;
uint32_t __pyx_v_k;
char *__pyx_v_s;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_seq_range", 0);
+ __Pyx_RefNannySetupContext("get_seq_range");
__Pyx_TraceCall("get_seq_range", __pyx_f[0], 2056);
- /* "pysam/csamtools.pyx":2061
+ /* "csamtools.pyx":2061
* cdef char * s
*
* if not src.core.l_qseq: # <<<<<<<<<<<<<<
__pyx_t_1 = (!__pyx_v_src->core.l_qseq);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2062
+ /* "csamtools.pyx":2062
*
* if not src.core.l_qseq:
* return None # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2064
+ /* "csamtools.pyx":2064
* return None
*
* seq = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
__pyx_v_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2065
+ /* "csamtools.pyx":2065
*
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq # <<<<<<<<<<<<<<
__pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2065; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_s = ((char *)__pyx_t_3);
- /* "pysam/csamtools.pyx":2066
+ /* "csamtools.pyx":2066
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq
* p = bam1_seq(src) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "pysam/csamtools.pyx":2068
+ /* "csamtools.pyx":2068
* p = bam1_seq(src)
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2071
+ /* "csamtools.pyx":2071
* # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
* # note: do not use string literal as it will be a python string
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] # <<<<<<<<<<<<<<
*
* return seq
*/
- (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_5pysam_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
+ (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
}
- /* "pysam/csamtools.pyx":2073
+ /* "csamtools.pyx":2073
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf]
*
* return seq # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.get_seq_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.get_seq_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_seq);
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2076
+/* "csamtools.pyx":2076
*
*
* cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
* cdef uint32_t k
*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
uint8_t *__pyx_v_p;
uint32_t __pyx_v_k;
char *__pyx_v_q;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_qual_range", 0);
+ __Pyx_RefNannySetupContext("get_qual_range");
__Pyx_TraceCall("get_qual_range", __pyx_f[0], 2076);
- /* "pysam/csamtools.pyx":2081
+ /* "csamtools.pyx":2081
* cdef char * q
*
* p = bam1_qual(src) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "pysam/csamtools.pyx":2082
+ /* "csamtools.pyx":2082
*
* p = bam1_qual(src)
* if p[0] == 0xff: # <<<<<<<<<<<<<<
__pyx_t_1 = ((__pyx_v_p[0]) == 0xff);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2083
+ /* "csamtools.pyx":2083
* p = bam1_qual(src)
* if p[0] == 0xff:
* return None # <<<<<<<<<<<<<<
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2085
+ /* "csamtools.pyx":2085
* return None
*
* qual = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
__pyx_v_qual = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2086
+ /* "csamtools.pyx":2086
*
* qual = PyBytes_FromStringAndSize(NULL, end - start)
* q = <char*>qual # <<<<<<<<<<<<<<
__pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_q = ((char *)__pyx_t_3);
- /* "pysam/csamtools.pyx":2088
+ /* "csamtools.pyx":2088
* q = <char*>qual
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2090
+ /* "csamtools.pyx":2090
* for k from start <= k < end:
* ## equivalent to t[i] + 33 (see bam.c)
* q[k-start] = p[k] + 33 # <<<<<<<<<<<<<<
(__pyx_v_q[(__pyx_v_k - __pyx_v_start)]) = ((__pyx_v_p[__pyx_v_k]) + 33);
}
- /* "pysam/csamtools.pyx":2092
+ /* "csamtools.pyx":2092
* q[k-start] = p[k] + 33
*
* return qual # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.get_qual_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.get_qual_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qual);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2124
+/* "csamtools.pyx":2124
*
* # Now only called when instances are created from Python
* def __init__(self): # <<<<<<<<<<<<<<
* self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) )
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 2124);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- /* "pysam/csamtools.pyx":2126
+ /* "csamtools.pyx":2126
* def __init__(self):
* # see bam_init1
* self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
* # allocate some memory
* # If size is 0, calloc does not return a pointer that can be passed to free()
*/
- __pyx_v_self->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "pysam/csamtools.pyx":2130
+ /* "csamtools.pyx":2130
* # If size is 0, calloc does not return a pointer that can be passed to free()
* # so allocate 40 bytes for a new read
* self._delegate.m_data = 40 # <<<<<<<<<<<<<<
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
* self._delegate.data_len = 0
*/
- __pyx_v_self->_delegate->m_data = 40;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data = 40;
- /* "pysam/csamtools.pyx":2131
+ /* "csamtools.pyx":2131
* # so allocate 40 bytes for a new read
* self._delegate.m_data = 40
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 ) # <<<<<<<<<<<<<<
* self._delegate.data_len = 0
*
*/
- __pyx_v_self->_delegate->data = ((uint8_t *)calloc(__pyx_v_self->_delegate->m_data, 1));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data = ((uint8_t *)calloc(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data, 1));
- /* "pysam/csamtools.pyx":2132
+ /* "csamtools.pyx":2132
* self._delegate.m_data = 40
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
* self._delegate.data_len = 0 # <<<<<<<<<<<<<<
*
* def __dealloc__(self):
*/
- __pyx_v_self->_delegate->data_len = 0;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data_len = 0;
__pyx_r = 0;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":2134
+/* "csamtools.pyx":2134
* self._delegate.data_len = 0
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
*
*/
-static void __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 2134);
- /* "pysam/csamtools.pyx":2135
+ /* "csamtools.pyx":2135
*
* def __dealloc__(self):
* bam_destroy1(self._delegate) # <<<<<<<<<<<<<<
*
* def __str__(self):
*/
- bam_destroy1(__pyx_v_self->_delegate);
+ bam_destroy1(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11AlignedRead_4__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
-struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__;
-#endif
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2137
+/* "csamtools.pyx":2137
* bam_destroy1(self._delegate)
*
* def __str__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_2__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_seq = NULL;
PyObject *__pyx_v_qual = NULL;
PyObject *__pyx_r = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 2137);
- /* "pysam/csamtools.pyx":2149
+ /* "csamtools.pyx":2149
* # sam-parsing is done in sam.c/bam_format1_core which
* # requires a valid header.
* if sys.version_info[0] < 3: # <<<<<<<<<<<<<<
__pyx_t_1 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_3, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_3, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":2150
+ /* "csamtools.pyx":2150
* # requires a valid header.
* if sys.version_info[0] < 3:
* seq = self.seq # <<<<<<<<<<<<<<
* qual = self.qual
* else:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_seq = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2151
+ /* "csamtools.pyx":2151
* if sys.version_info[0] < 3:
* seq = self.seq
* qual = self.qual # <<<<<<<<<<<<<<
* else:
* seq = self.seq.decode('ascii')
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2153
+ /* "csamtools.pyx":2153
* qual = self.qual
* else:
* seq = self.seq.decode('ascii') # <<<<<<<<<<<<<<
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_seq = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2154
+ /* "csamtools.pyx":2154
* else:
* seq = self.seq.decode('ascii')
* qual = self.qual.decode('ascii') # <<<<<<<<<<<<<<
* return "\t".join(map(str, (self.qname,
* self.flag,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2155
+ /* "csamtools.pyx":2155
* seq = self.seq.decode('ascii')
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname, # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":2156
+ /* "csamtools.pyx":2156
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname,
* self.flag, # <<<<<<<<<<<<<<
* self.rname,
* self.pos,
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- /* "pysam/csamtools.pyx":2157
+ /* "csamtools.pyx":2157
* return "\t".join(map(str, (self.qname,
* self.flag,
* self.rname, # <<<<<<<<<<<<<<
* self.pos,
* self.mapq,
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- /* "pysam/csamtools.pyx":2158
+ /* "csamtools.pyx":2158
* self.flag,
* self.rname,
* self.pos, # <<<<<<<<<<<<<<
* self.mapq,
* self.cigar,
*/
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "pysam/csamtools.pyx":2159
+ /* "csamtools.pyx":2159
* self.rname,
* self.pos,
* self.mapq, # <<<<<<<<<<<<<<
* self.cigar,
* self.mrnm,
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/csamtools.pyx":2160
+ /* "csamtools.pyx":2160
* self.pos,
* self.mapq,
* self.cigar, # <<<<<<<<<<<<<<
* self.mrnm,
* self.mpos,
*/
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- /* "pysam/csamtools.pyx":2161
+ /* "csamtools.pyx":2161
* self.mapq,
* self.cigar,
* self.mrnm, # <<<<<<<<<<<<<<
* self.mpos,
* self.rlen,
*/
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- /* "pysam/csamtools.pyx":2162
+ /* "csamtools.pyx":2162
* self.cigar,
* self.mrnm,
* self.mpos, # <<<<<<<<<<<<<<
* self.rlen,
* seq,
*/
- __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- /* "pysam/csamtools.pyx":2163
+ /* "csamtools.pyx":2163
* self.mrnm,
* self.mpos,
* self.rlen, # <<<<<<<<<<<<<<
* seq,
* qual,
*/
- __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- /* "pysam/csamtools.pyx":2166
+ /* "csamtools.pyx":2166
* seq,
* qual,
* self.tags ))) # <<<<<<<<<<<<<<
*
* def compare(self, AlignedRead other):
*/
- __pyx_t_12 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__pyx_t_13 = PyTuple_New(12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_4);
__pyx_t_11 = 0;
__pyx_t_12 = 0;
__pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_12));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_12, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
__pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_12));
PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_13);
__Pyx_GIVEREF(__pyx_t_13);
__pyx_t_13 = 0;
__Pyx_XDECREF(__pyx_t_11);
__Pyx_XDECREF(__pyx_t_12);
__Pyx_XDECREF(__pyx_t_13);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_seq);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11AlignedRead_6compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("compare (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_other));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2168
+/* "csamtools.pyx":2168
* self.tags )))
*
* def compare(self, AlignedRead other): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_other) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_3compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
int __pyx_v_retval;
bam1_t *__pyx_v_t;
bam1_t *__pyx_v_o;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("compare", 0);
+ __Pyx_RefNannySetupContext("compare");
__Pyx_TraceCall("compare", __pyx_f[0], 2168);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2174
+ /* "csamtools.pyx":2174
* cdef bam1_t *t, *o
*
* t = self._delegate # <<<<<<<<<<<<<<
* o = other._delegate
*
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_t = __pyx_t_1;
+ __pyx_v_t = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2175
+ /* "csamtools.pyx":2175
*
* t = self._delegate
* o = other._delegate # <<<<<<<<<<<<<<
*
* # uncomment for debugging purposes
*/
- __pyx_t_1 = __pyx_v_other->_delegate;
- __pyx_v_o = __pyx_t_1;
+ __pyx_v_o = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other)->_delegate;
- /* "pysam/csamtools.pyx":2187
+ /* "csamtools.pyx":2187
*
* # Fast-path test for object identity
* if t==o: # <<<<<<<<<<<<<<
* return 0
*
*/
- __pyx_t_2 = (__pyx_v_t == __pyx_v_o);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_t == __pyx_v_o);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2188
+ /* "csamtools.pyx":2188
* # Fast-path test for object identity
* if t==o:
* return 0 # <<<<<<<<<<<<<<
__Pyx_INCREF(__pyx_int_0);
__pyx_r = __pyx_int_0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2190
+ /* "csamtools.pyx":2190
* return 0
*
* retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t)) # <<<<<<<<<<<<<<
*/
__pyx_v_retval = memcmp((&__pyx_v_t->core), (&__pyx_v_o->core), (sizeof(bam1_core_t)));
- /* "pysam/csamtools.pyx":2192
+ /* "csamtools.pyx":2192
* retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
*
* if retval: return retval # <<<<<<<<<<<<<<
*/
if (__pyx_v_retval) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":2193
+ /* "csamtools.pyx":2193
*
* if retval: return retval
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len) # <<<<<<<<<<<<<<
*/
__pyx_v_retval = ((__pyx_v_t->data_len > __pyx_v_o->data_len) - (__pyx_v_t->data_len < __pyx_v_o->data_len));
- /* "pysam/csamtools.pyx":2194
+ /* "csamtools.pyx":2194
* if retval: return retval
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
* if retval: return retval # <<<<<<<<<<<<<<
*/
if (__pyx_v_retval) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":2195
+ /* "csamtools.pyx":2195
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
* if retval: return retval
* return memcmp(t.data, o.data, t.data_len) # <<<<<<<<<<<<<<
* # Disabled so long as __cmp__ is a special method
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(memcmp(__pyx_v_t->data, __pyx_v_o->data, __pyx_v_t->data_len)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyInt_FromLong(memcmp(__pyx_v_t->data, __pyx_v_o->data, __pyx_v_t->data_len)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static Py_hash_t __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self); /*proto*/
-static Py_hash_t __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self) {
- Py_hash_t __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2198
+/* "csamtools.pyx":2198
*
* # Disabled so long as __cmp__ is a special method
* def __hash__(self): # <<<<<<<<<<<<<<
*
*/
-static Py_hash_t __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_self); /*proto*/
+static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_self) {
Py_hash_t __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__hash__", 0);
+ __Pyx_RefNannySetupContext("__hash__");
__Pyx_TraceCall("__hash__", __pyx_f[0], 2198);
- /* "pysam/csamtools.pyx":2199
+ /* "csamtools.pyx":2199
* # Disabled so long as __cmp__ is a special method
* def __hash__(self):
* return _Py_HashPointer(<void *>self) # <<<<<<<<<<<<<<
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2203
+/* "csamtools.pyx":2203
* property qname:
* """the query name (None if not present)"""
* def __get__(self): # <<<<<<<<<<<<<<
* src = self._delegate
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2203);
- /* "pysam/csamtools.pyx":2205
+ /* "csamtools.pyx":2205
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.l_qname == 0: return None
* return _charptr_to_str(<char *>bam1_qname( src ))
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2206
+ /* "csamtools.pyx":2206
* cdef bam1_t * src
* src = self._delegate
* if src.core.l_qname == 0: return None # <<<<<<<<<<<<<<
* return _charptr_to_str(<char *>bam1_qname( src ))
*
*/
- __pyx_t_2 = (__pyx_v_src->core.l_qname == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.l_qname == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2207
+ /* "csamtools.pyx":2207
* src = self._delegate
* if src.core.l_qname == 0: return None
* return _charptr_to_str(<char *>bam1_qname( src )) # <<<<<<<<<<<<<<
* def __set__(self, qname ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_5pysam_9csamtools__charptr_to_str(((char *)bam1_qname(__pyx_v_src))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str(((char *)bam1_qname(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2209
+/* "csamtools.pyx":2209
* return _charptr_to_str(<char *>bam1_qname( src ))
*
* def __set__(self, qname ): # <<<<<<<<<<<<<<
* qname = _force_bytes(qname)
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname) {
+static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
bam1_t *__pyx_v_src;
int __pyx_v_l;
char *__pyx_v_p;
Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- bam1_t *__pyx_t_6;
- char *__pyx_t_7;
+ char *__pyx_t_6;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2209);
__Pyx_INCREF(__pyx_v_qname);
- /* "pysam/csamtools.pyx":2210
+ /* "csamtools.pyx":2210
*
* def __set__(self, qname ):
* if qname == None or len(qname) == 0: return # <<<<<<<<<<<<<<
* qname = _force_bytes(qname)
* cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2211
+ /* "csamtools.pyx":2211
* def __set__(self, qname ):
* if qname == None or len(qname) == 0: return
* qname = _force_bytes(qname) # <<<<<<<<<<<<<<
* cdef bam1_t * src
* cdef int l
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_qname)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_qname)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_qname);
__pyx_v_qname = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2216
+ /* "csamtools.pyx":2216
* cdef char * p
*
* src = self._delegate # <<<<<<<<<<<<<<
* p = bam1_qname( src )
*
*/
- __pyx_t_6 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_6;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2217
+ /* "csamtools.pyx":2217
*
* src = self._delegate
* p = bam1_qname( src ) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_qname(__pyx_v_src);
- /* "pysam/csamtools.pyx":2220
+ /* "csamtools.pyx":2220
*
* # the qname is \0 terminated
* l = len(qname) + 1 # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_l = (__pyx_t_3 + 1);
- /* "pysam/csamtools.pyx":2224
+ /* "csamtools.pyx":2224
* src.core.l_qname,
* l,
* <uint8_t*>p ) # <<<<<<<<<<<<<<
*/
pysam_bam_update(__pyx_v_src, __pyx_v_src->core.l_qname, __pyx_v_l, ((uint8_t *)__pyx_v_p));
- /* "pysam/csamtools.pyx":2226
+ /* "csamtools.pyx":2226
* <uint8_t*>p )
*
* src.core.l_qname = l # <<<<<<<<<<<<<<
*/
__pyx_v_src->core.l_qname = __pyx_v_l;
- /* "pysam/csamtools.pyx":2230
+ /* "csamtools.pyx":2230
* # re-acquire pointer to location in memory
* # as it might have moved
* p = bam1_qname(src) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_qname(__pyx_v_src);
- /* "pysam/csamtools.pyx":2232
+ /* "csamtools.pyx":2232
* p = bam1_qname(src)
*
* strncpy( p, qname, l ) # <<<<<<<<<<<<<<
*
* property cigar:
*/
- __pyx_t_7 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy(__pyx_v_p, __pyx_t_7, __pyx_v_l);
+ __pyx_t_6 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy(__pyx_v_p, __pyx_t_6, __pyx_v_l);
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qname);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2259
+/* "csamtools.pyx":2259
*
* """
* def __get__(self): # <<<<<<<<<<<<<<
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self) {
uint32_t *__pyx_v_cigar_p;
bam1_t *__pyx_v_src;
PyObject *__pyx_v_op = 0;
int __pyx_v_k;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- uint32_t __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ uint32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2259);
- /* "pysam/csamtools.pyx":2265
+ /* "csamtools.pyx":2265
* cdef int k
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return None
*
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2266
+ /* "csamtools.pyx":2266
*
* src = self._delegate
* if src.core.n_cigar == 0: return None # <<<<<<<<<<<<<<
*
* cigar = []
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2268
+ /* "csamtools.pyx":2268
* if src.core.n_cigar == 0: return None
*
* cigar = [] # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_cigar = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_cigar = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2269
+ /* "csamtools.pyx":2269
*
* cigar = []
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2270
+ /* "csamtools.pyx":2270
* cigar = []
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_4 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
+ __pyx_t_3 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2271
+ /* "csamtools.pyx":2271
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l))
*/
- __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_op = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2272
+ /* "csamtools.pyx":2272
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
* cigar.append((op, l))
* return cigar
*/
- __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_l = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2273
+ /* "csamtools.pyx":2273
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l)) # <<<<<<<<<<<<<<
* return cigar
*
*/
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_op);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_op);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op);
__Pyx_GIVEREF(__pyx_v_op);
__Pyx_INCREF(__pyx_v_l);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_l);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_l);
__Pyx_GIVEREF(__pyx_v_l);
- __pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
- /* "pysam/csamtools.pyx":2274
+ /* "csamtools.pyx":2274
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l))
* return cigar # <<<<<<<<<<<<<<
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigar.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_op);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_values));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2276
+/* "csamtools.pyx":2276
* return cigar
*
* def __set__(self, values ): # <<<<<<<<<<<<<<
* cdef uint32_t * p
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values) {
+static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
uint32_t *__pyx_v_p;
bam1_t *__pyx_v_src;
PyObject *__pyx_v_op = 0;
Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- bam1_t *__pyx_t_6;
- PyObject *(*__pyx_t_7)(PyObject *);
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
PyObject *__pyx_t_9 = NULL;
PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- PyObject *(*__pyx_t_12)(PyObject *);
- uint32_t __pyx_t_13;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ uint32_t __pyx_t_12;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2276);
- /* "pysam/csamtools.pyx":2277
+ /* "csamtools.pyx":2277
*
* def __set__(self, values ):
* if values == None or len(values) == 0: return # <<<<<<<<<<<<<<
* cdef uint32_t * p
* cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2283
+ /* "csamtools.pyx":2283
* cdef int k
*
* k = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_k = 0;
- /* "pysam/csamtools.pyx":2285
+ /* "csamtools.pyx":2285
* k = 0
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* # get location of cigar string
*/
- __pyx_t_6 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_6;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2288
+ /* "csamtools.pyx":2288
*
* # get location of cigar string
* p = bam1_cigar(src) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2293
+ /* "csamtools.pyx":2293
* pysam_bam_update( src,
* src.core.n_cigar * 4,
* len(values) * 4, # <<<<<<<<<<<<<<
*/
__pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2294
+ /* "csamtools.pyx":2294
* src.core.n_cigar * 4,
* len(values) * 4,
* <uint8_t*>p ) # <<<<<<<<<<<<<<
*/
pysam_bam_update(__pyx_v_src, (__pyx_v_src->core.n_cigar * 4), (__pyx_t_3 * 4), ((uint8_t *)__pyx_v_p));
- /* "pysam/csamtools.pyx":2297
+ /* "csamtools.pyx":2297
*
* # length is number of cigar operations, not bytes
* src.core.n_cigar = len(values) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_src->core.n_cigar = __pyx_t_3;
- /* "pysam/csamtools.pyx":2301
+ /* "csamtools.pyx":2301
* # re-acquire pointer to location in memory
* # as it might have moved
* p = bam1_cigar(src) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2304
+ /* "csamtools.pyx":2304
*
* # insert cigar operations
* for op, l in values: # <<<<<<<<<<<<<<
*/
if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
__pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
- __pyx_t_7 = NULL;
+ __pyx_t_6 = NULL;
} else {
__pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_7 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_7 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else {
- __pyx_t_8 = __pyx_t_7(__pyx_t_1);
- if (unlikely(!__pyx_t_8)) {
+ __pyx_t_7 = __pyx_t_6(__pyx_t_1);
+ if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_7);
}
- if ((likely(PyTuple_CheckExact(__pyx_t_8))) || (PyList_CheckExact(__pyx_t_8))) {
- PyObject* sequence = __pyx_t_8;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
+ if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
+ PyObject* sequence = __pyx_t_7;
if (likely(PyTuple_CheckExact(sequence))) {
- __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
} else {
- __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
}
+ __Pyx_INCREF(__pyx_t_8);
__Pyx_INCREF(__pyx_t_9);
- __Pyx_INCREF(__pyx_t_10);
- #else
- __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- } else
- {
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ } else {
Py_ssize_t index = -1;
- __pyx_t_11 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed;
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_8);
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_op = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_l = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":2305
+ /* "csamtools.pyx":2305
* # insert cigar operations
* for op, l in values:
* p[k] = l << BAM_CIGAR_SHIFT | op # <<<<<<<<<<<<<<
* k += 1
*
*/
- __pyx_t_8 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyNumber_Or(__pyx_t_8, __pyx_v_op); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_13 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_10); if (unlikely((__pyx_t_13 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- (__pyx_v_p[__pyx_v_k]) = __pyx_t_13;
+ __pyx_t_7 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = PyNumber_Or(__pyx_t_7, __pyx_v_op); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_12 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ (__pyx_v_p[__pyx_v_k]) = __pyx_t_12;
- /* "pysam/csamtools.pyx":2306
+ /* "csamtools.pyx":2306
* for op, l in values:
* p[k] = l << BAM_CIGAR_SHIFT | op
* k += 1 # <<<<<<<<<<<<<<
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2309
+ /* "csamtools.pyx":2309
*
* ## setting the cigar string also updates the "bin" attribute
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, p)) # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigar.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_op);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2316
+/* "csamtools.pyx":2316
* Returns the empty string if not present.
* '''
* def __get__(self): # <<<<<<<<<<<<<<
* if c == None: return ""
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_c = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_v_y = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2316);
- /* "pysam/csamtools.pyx":2317
+ /* "csamtools.pyx":2317
* '''
* def __get__(self):
* c = self.cigar # <<<<<<<<<<<<<<
* if c == None: return ""
* else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_c = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2318
+ /* "csamtools.pyx":2318
* def __get__(self):
* c = self.cigar
* if c == None: return "" # <<<<<<<<<<<<<<
* else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_c, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_c, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_16));
__pyx_r = ((PyObject *)__pyx_kp_s_16);
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2319
+ /* "csamtools.pyx":2319
* c = self.cigar
* if c == None: return ""
* else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c]) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
if (PyList_CheckExact(__pyx_v_c) || PyTuple_CheckExact(__pyx_v_c)) {
__pyx_t_4 = __pyx_v_c; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
__pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) {
+ if (PyList_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
+ } else if (PyTuple_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
} else {
__pyx_t_7 = __pyx_t_6(__pyx_t_4);
if (unlikely(!__pyx_t_7)) {
}
if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
PyObject* sequence = __pyx_t_7;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_8 = PyList_GET_ITEM(sequence, 0);
__pyx_t_9 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_8);
__Pyx_INCREF(__pyx_t_9);
- #else
- __pyx_t_8 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = NULL;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_11 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_8;
__pyx_v_y = __pyx_t_9;
__pyx_t_9 = 0;
__pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromLong((__pyx_v_5pysam_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromLong((__pyx_v_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_y);
__pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_135), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- if (unlikely(__Pyx_PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
__pyx_t_3 = 0;
goto __pyx_L0;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigarstring.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigarstring.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_c);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_cigar));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2321
+/* "csamtools.pyx":2321
* else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
*
* def __set__(self, cigar): # <<<<<<<<<<<<<<
* parts = CIGAR_REGEX.findall( cigar )
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar) {
+static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
PyObject *__pyx_v_parts = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_v_y = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2321);
- /* "pysam/csamtools.pyx":2322
+ /* "csamtools.pyx":2322
*
* def __set__(self, cigar):
* if cigar == None or len(cigar) == 0: self.cigar = [] # <<<<<<<<<<<<<<
* parts = CIGAR_REGEX.findall( cigar )
* self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ]
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_cigar, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_cigar, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
}
if (__pyx_t_5) {
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2323
+ /* "csamtools.pyx":2323
* def __set__(self, cigar):
* if cigar == None or len(cigar) == 0: self.cigar = []
* parts = CIGAR_REGEX.findall( cigar ) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_cigar);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_cigar);
__Pyx_GIVEREF(__pyx_v_cigar);
__pyx_v_parts = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":2324
+ /* "csamtools.pyx":2324
* if cigar == None or len(cigar) == 0: self.cigar = []
* parts = CIGAR_REGEX.findall( cigar )
* self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ] # <<<<<<<<<<<<<<
* property seq:
*/
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
if (PyList_CheckExact(__pyx_v_parts) || PyTuple_CheckExact(__pyx_v_parts)) {
__pyx_t_1 = __pyx_v_parts; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
__pyx_t_8 = NULL;
__pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
} else {
__pyx_t_6 = __pyx_t_8(__pyx_t_1);
if (unlikely(!__pyx_t_6)) {
}
if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
PyObject* sequence = __pyx_t_6;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_9 = PyList_GET_ITEM(sequence, 0);
__pyx_t_10 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_10);
- #else
- __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_11 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed;
+ index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_9;
__pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR2CODE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
__Pyx_INCREF(__pyx_v_x);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_x);
__Pyx_GIVEREF(__pyx_v_x);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_INCREF(__pyx_v_y);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_y);
__Pyx_GIVEREF(__pyx_v_y);
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_10 = 0;
__pyx_t_6 = 0;
- if (unlikely(__Pyx_PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_9))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_9))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = ((PyObject *)__pyx_t_7);
- __Pyx_INCREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = 0;
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigarstring.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.cigarstring.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_parts);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2330
+/* "csamtools.pyx":2330
*
* In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
* def __get__(self): # <<<<<<<<<<<<<<
* cdef char * s
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2330);
- /* "pysam/csamtools.pyx":2333
+ /* "csamtools.pyx":2333
* cdef bam1_t * src
* cdef char * s
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2335
+ /* "csamtools.pyx":2335
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* return get_seq_range(src, 0, src.core.l_qseq)
*/
- __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2337
+ /* "csamtools.pyx":2337
* if src.core.l_qseq == 0: return None
*
* return get_seq_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
* def __set__(self,seq):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.seq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.seq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_seq));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2339
+/* "csamtools.pyx":2339
* return get_seq_range(src, 0, src.core.l_qseq)
*
* def __set__(self,seq): # <<<<<<<<<<<<<<
* # if no quality information is present, the first byte says 0xff.
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq) {
+static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_p;
char *__pyx_v_s;
Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- bam1_t *__pyx_t_6;
- int __pyx_t_7;
- char *__pyx_t_8;
- long __pyx_t_9;
+ int __pyx_t_6;
+ char *__pyx_t_7;
+ long __pyx_t_8;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2339);
__Pyx_INCREF(__pyx_v_seq);
- /* "pysam/csamtools.pyx":2343
+ /* "csamtools.pyx":2343
* # if no quality information is present, the first byte says 0xff.
*
* if seq == None or len(seq) == 0: return # <<<<<<<<<<<<<<
* seq = _force_bytes(seq)
* cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2344
+ /* "csamtools.pyx":2344
*
* if seq == None or len(seq) == 0: return
* seq = _force_bytes(seq) # <<<<<<<<<<<<<<
* cdef bam1_t * src
* cdef uint8_t * p
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_seq)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_seq)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_seq);
__pyx_v_seq = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2350
+ /* "csamtools.pyx":2350
* cdef int l, k, nbytes_new, nbytes_old
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* l = len(seq)
*/
- __pyx_t_6 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_6;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2352
+ /* "csamtools.pyx":2352
* src = self._delegate
*
* l = len(seq) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_l = __pyx_t_3;
- /* "pysam/csamtools.pyx":2356
+ /* "csamtools.pyx":2356
* # as the sequence is stored in half-bytes, the total length (sequence
* # plus quality scores) is (l+1)/2 + l
* nbytes_new = (l+1)/2 + l # <<<<<<<<<<<<<<
*/
__pyx_v_nbytes_new = (__Pyx_div_long((__pyx_v_l + 1), 2) + __pyx_v_l);
- /* "pysam/csamtools.pyx":2357
+ /* "csamtools.pyx":2357
* # plus quality scores) is (l+1)/2 + l
* nbytes_new = (l+1)/2 + l
* nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq # <<<<<<<<<<<<<<
*/
__pyx_v_nbytes_old = (__Pyx_div_long((__pyx_v_src->core.l_qseq + 1), 2) + __pyx_v_src->core.l_qseq);
- /* "pysam/csamtools.pyx":2359
+ /* "csamtools.pyx":2359
* nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
* # acquire pointer to location in memory
* p = bam1_seq( src ) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "pysam/csamtools.pyx":2360
+ /* "csamtools.pyx":2360
* # acquire pointer to location in memory
* p = bam1_seq( src )
* src.core.l_qseq = l # <<<<<<<<<<<<<<
*/
__pyx_v_src->core.l_qseq = __pyx_v_l;
- /* "pysam/csamtools.pyx":2365
+ /* "csamtools.pyx":2365
* nbytes_old,
* nbytes_new,
* p) # <<<<<<<<<<<<<<
*/
pysam_bam_update(__pyx_v_src, __pyx_v_nbytes_old, __pyx_v_nbytes_new, __pyx_v_p);
- /* "pysam/csamtools.pyx":2368
+ /* "csamtools.pyx":2368
* # re-acquire pointer to location in memory
* # as it might have moved
* p = bam1_seq( src ) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "pysam/csamtools.pyx":2369
+ /* "csamtools.pyx":2369
* # as it might have moved
* p = bam1_seq( src )
* for k from 0 <= k < nbytes_new: p[k] = 0 # <<<<<<<<<<<<<<
* # convert to C string
* s = seq
*/
- __pyx_t_7 = __pyx_v_nbytes_new;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_7; __pyx_v_k++) {
+ __pyx_t_6 = __pyx_v_nbytes_new;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
(__pyx_v_p[__pyx_v_k]) = 0;
}
- /* "pysam/csamtools.pyx":2371
+ /* "csamtools.pyx":2371
* for k from 0 <= k < nbytes_new: p[k] = 0
* # convert to C string
* s = seq # <<<<<<<<<<<<<<
* for k from 0 <= k < l:
* p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
*/
- __pyx_t_8 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_s = __pyx_t_8;
+ __pyx_t_7 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = __pyx_t_7;
- /* "pysam/csamtools.pyx":2372
+ /* "csamtools.pyx":2372
* # convert to C string
* s = seq
* for k from 0 <= k < l: # <<<<<<<<<<<<<<
* p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
*
*/
- __pyx_t_7 = __pyx_v_l;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_7; __pyx_v_k++) {
+ __pyx_t_6 = __pyx_v_l;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2373
+ /* "csamtools.pyx":2373
* s = seq
* for k from 0 <= k < l:
* p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) # <<<<<<<<<<<<<<
*
* # erase qualities
*/
- __pyx_t_9 = __Pyx_div_long(__pyx_v_k, 2);
- (__pyx_v_p[__pyx_t_9]) = ((__pyx_v_p[__pyx_t_9]) | (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))));
+ __pyx_t_8 = __Pyx_div_long(__pyx_v_k, 2);
+ (__pyx_v_p[__pyx_t_8]) = ((__pyx_v_p[__pyx_t_8]) | (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))));
}
- /* "pysam/csamtools.pyx":2376
+ /* "csamtools.pyx":2376
*
* # erase qualities
* p = bam1_qual( src ) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "pysam/csamtools.pyx":2377
+ /* "csamtools.pyx":2377
* # erase qualities
* p = bam1_qual( src )
* p[0] = 0xff # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.seq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.seq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_seq);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2384
+/* "csamtools.pyx":2384
*
* In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
* def __get__(self): # <<<<<<<<<<<<<<
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2384);
- /* "pysam/csamtools.pyx":2389
+ /* "csamtools.pyx":2389
* cdef char * q
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2391
+ /* "csamtools.pyx":2391
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* return get_qual_range(src, 0, src.core.l_qseq)
*/
- __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2393
+ /* "csamtools.pyx":2393
* if src.core.l_qseq == 0: return None
*
* return get_qual_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
* def __set__(self,qual):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2395
+/* "csamtools.pyx":2395
* return get_qual_range(src, 0, src.core.l_qseq)
*
* def __set__(self,qual): # <<<<<<<<<<<<<<
* cdef bam1_t * src
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
+static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_p;
char *__pyx_v_q;
int __pyx_v_l;
int __pyx_r;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- Py_ssize_t __pyx_t_4;
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ Py_ssize_t __pyx_t_3;
+ int __pyx_t_4;
int __pyx_t_5;
- int __pyx_t_6;
- char *__pyx_t_7;
+ char *__pyx_t_6;
+ PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- int __pyx_t_10;
+ int __pyx_t_9;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2395);
__Pyx_INCREF(__pyx_v_qual);
- /* "pysam/csamtools.pyx":2402
+ /* "csamtools.pyx":2402
* cdef int k
*
* src = self._delegate # <<<<<<<<<<<<<<
* p = bam1_qual( src )
* if qual == None or len(qual) == 0:
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2403
+ /* "csamtools.pyx":2403
*
* src = self._delegate
* p = bam1_qual( src ) # <<<<<<<<<<<<<<
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "pysam/csamtools.pyx":2404
+ /* "csamtools.pyx":2404
* src = self._delegate
* p = bam1_qual( src )
* if qual == None or len(qual) == 0: # <<<<<<<<<<<<<<
* # if absent - set to 0xff
* p[0] = 0xff
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!__pyx_t_3) {
- __pyx_t_4 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = (__pyx_t_4 == 0);
- __pyx_t_6 = __pyx_t_5;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!__pyx_t_2) {
+ __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__pyx_t_3 == 0);
+ __pyx_t_5 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_3;
+ __pyx_t_5 = __pyx_t_2;
}
- if (__pyx_t_6) {
+ if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2406
+ /* "csamtools.pyx":2406
* if qual == None or len(qual) == 0:
* # if absent - set to 0xff
* p[0] = 0xff # <<<<<<<<<<<<<<
*/
(__pyx_v_p[0]) = 0xff;
- /* "pysam/csamtools.pyx":2407
+ /* "csamtools.pyx":2407
* # if absent - set to 0xff
* p[0] = 0xff
* return # <<<<<<<<<<<<<<
*/
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2408
+ /* "csamtools.pyx":2408
* p[0] = 0xff
* return
* qual = _force_bytes(qual) # <<<<<<<<<<<<<<
* cdef int l
* # convert to C string
*/
- __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_qual)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_qual)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_qual);
- __pyx_v_qual = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_qual = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2411
+ /* "csamtools.pyx":2411
* cdef int l
* # convert to C string
* q = qual # <<<<<<<<<<<<<<
* l = len(qual)
* if src.core.l_qseq != l:
*/
- __pyx_t_7 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_q = __pyx_t_7;
+ __pyx_t_6 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_q = __pyx_t_6;
- /* "pysam/csamtools.pyx":2412
+ /* "csamtools.pyx":2412
* # convert to C string
* q = qual
* l = len(qual) # <<<<<<<<<<<<<<
* if src.core.l_qseq != l:
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_l = __pyx_t_4;
+ __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_l = __pyx_t_3;
- /* "pysam/csamtools.pyx":2413
+ /* "csamtools.pyx":2413
* q = qual
* l = len(qual)
* if src.core.l_qseq != l: # <<<<<<<<<<<<<<
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
* assert src.core.l_qseq == l
*/
- __pyx_t_6 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
- if (__pyx_t_6) {
+ __pyx_t_5 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
+ if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2414
+ /* "csamtools.pyx":2414
* l = len(qual)
* if src.core.l_qseq != l:
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) # <<<<<<<<<<<<<<
* assert src.core.l_qseq == l
* for k from 0 <= k < l:
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_2 = 0;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_136), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_1 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_136), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":2415
+ /* "csamtools.pyx":2415
* if src.core.l_qseq != l:
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
* assert src.core.l_qseq == l # <<<<<<<<<<<<<<
}
#endif
- /* "pysam/csamtools.pyx":2416
+ /* "csamtools.pyx":2416
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
* assert src.core.l_qseq == l
* for k from 0 <= k < l: # <<<<<<<<<<<<<<
* p[k] = <uint8_t>q[k] - 33
*
*/
- __pyx_t_10 = __pyx_v_l;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_10; __pyx_v_k++) {
+ __pyx_t_9 = __pyx_v_l;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_9; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2417
+ /* "csamtools.pyx":2417
* assert src.core.l_qseq == l
* for k from 0 <= k < l:
* p[k] = <uint8_t>q[k] - 33 # <<<<<<<<<<<<<<
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qual.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qual.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qual);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2431
+/* "csamtools.pyx":2431
* were not considered for alignment may have been retained."""
*
* def __get__(self): # <<<<<<<<<<<<<<
* cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- int32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_1;
+ int32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2431);
- /* "pysam/csamtools.pyx":2436
+ /* "csamtools.pyx":2436
* cdef char * s
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2438
+ /* "csamtools.pyx":2438
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* start = query_start(src)
*/
- __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2440
+ /* "csamtools.pyx":2440
* if src.core.l_qseq == 0: return None
*
* start = query_start(src) # <<<<<<<<<<<<<<
* end = query_end(src)
*
*/
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_start = __pyx_t_3;
+ __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_start = __pyx_t_2;
- /* "pysam/csamtools.pyx":2441
+ /* "csamtools.pyx":2441
*
* start = query_start(src)
* end = query_end(src) # <<<<<<<<<<<<<<
*
* return get_seq_range(src, start, end)
*/
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_end = __pyx_t_3;
+ __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_end = __pyx_t_2;
- /* "pysam/csamtools.pyx":2443
+ /* "csamtools.pyx":2443
* end = query_end(src)
*
* return get_seq_range(src, start, end) # <<<<<<<<<<<<<<
* property qqual:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_5pysam_9csamtools_get_seq_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_r = __pyx_t_4;
- __pyx_t_4 = 0;
+ __pyx_t_3 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.query.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.AlignedRead.query.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2449
+/* "csamtools.pyx":2449
*
* In Python 3, this property is of type bytes."""
* def __get__(self): # <<<<<<<<<<<<<<
* cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- int32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_1;
+ int32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2449);
- /* "pysam/csamtools.pyx":2453
+ /* "csamtools.pyx":2453
* cdef uint32_t start, end
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2455
+ /* "csamtools.pyx":2455
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* start = query_start(src)
*/
- __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2457
+ /* "csamtools.pyx":2457
* if src.core.l_qseq == 0: return None
*
* start = query_start(src) # <<<<<<<<<<<<<<
* end = query_end(src)
*
*/
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_start = __pyx_t_3;
+ __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_start = __pyx_t_2;
- /* "pysam/csamtools.pyx":2458
+ /* "csamtools.pyx":2458
*
* start = query_start(src)
* end = query_end(src) # <<<<<<<<<<<<<<
*
* return get_qual_range(src, start, end)
*/
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_end = __pyx_t_3;
+ __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_end = __pyx_t_2;
- /* "pysam/csamtools.pyx":2460
+ /* "csamtools.pyx":2460
* end = query_end(src)
*
* return get_qual_range(src, start, end) # <<<<<<<<<<<<<<
* property qstart:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_5pysam_9csamtools_get_qual_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_r = __pyx_t_4;
- __pyx_t_4 = 0;
+ __pyx_t_3 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qqual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qqual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2464
+/* "csamtools.pyx":2464
* property qstart:
* """start index of the aligned query portion of the sequence (0-based, inclusive)"""
* def __get__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2464);
- /* "pysam/csamtools.pyx":2465
+ /* "csamtools.pyx":2465
* """start index of the aligned query portion of the sequence (0-based, inclusive)"""
* def __get__(self):
* return query_start(self._delegate) # <<<<<<<<<<<<<<
* property qend:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_query_start(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qstart.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qstart.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2469
+/* "csamtools.pyx":2469
* property qend:
* """end index of the aligned query portion of the sequence (0-based, exclusive)"""
* def __get__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2469);
- /* "pysam/csamtools.pyx":2470
+ /* "csamtools.pyx":2470
* """end index of the aligned query portion of the sequence (0-based, exclusive)"""
* def __get__(self):
* return query_end(self._delegate) # <<<<<<<<<<<<<<
* property qlen:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_query_end(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2474
+/* "csamtools.pyx":2474
* property qlen:
* """Length of the aligned query sequence"""
* def __get__(self): # <<<<<<<<<<<<<<
* src = self._delegate
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
+ int32_t __pyx_t_1;
int32_t __pyx_t_2;
- int32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2474);
- /* "pysam/csamtools.pyx":2476
+ /* "csamtools.pyx":2476
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* return query_end(src)-query_start(src)
*
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2477
+ /* "csamtools.pyx":2477
* cdef bam1_t * src
* src = self._delegate
* return query_end(src)-query_start(src) # <<<<<<<<<<<<<<
* property tags:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = PyInt_FromLong((__pyx_t_2 - __pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_r = __pyx_t_4;
- __pyx_t_4 = 0;
+ __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong((__pyx_t_1 - __pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools.AlignedRead.qlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2494
+/* "csamtools.pyx":2494
* multiple times.
* """
* def __get__(self): # <<<<<<<<<<<<<<
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_s;
char __pyx_v_auxtag[3];
PyObject *__pyx_v_value = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- char __pyx_t_4;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ char __pyx_t_3;
+ int __pyx_t_4;
int __pyx_t_5;
- int __pyx_t_6;
- PyObject *__pyx_t_7 = NULL;
- Py_ssize_t __pyx_t_8;
+ PyObject *__pyx_t_6 = NULL;
+ Py_ssize_t __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
PyObject *__pyx_t_9 = NULL;
PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- PyObject *(*__pyx_t_12)(PyObject *);
- uint8_t __pyx_t_13;
- int32_t __pyx_t_14;
- int __pyx_t_15;
+ PyObject *(*__pyx_t_11)(PyObject *);
+ uint8_t __pyx_t_12;
+ int32_t __pyx_t_13;
+ int __pyx_t_14;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2494);
- /* "pysam/csamtools.pyx":2503
+ /* "csamtools.pyx":2503
* cdef int32_t nvalues
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.l_aux == 0: return []
* s = bam1_aux( src )
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2504
+ /* "csamtools.pyx":2504
*
* src = self._delegate
* if src.l_aux == 0: return [] # <<<<<<<<<<<<<<
* s = bam1_aux( src )
* result = []
*/
- __pyx_t_2 = (__pyx_v_src->l_aux == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->l_aux == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2505
+ /* "csamtools.pyx":2505
* src = self._delegate
* if src.l_aux == 0: return []
* s = bam1_aux( src ) # <<<<<<<<<<<<<<
*/
__pyx_v_s = bam1_aux(__pyx_v_src);
- /* "pysam/csamtools.pyx":2506
+ /* "csamtools.pyx":2506
* if src.l_aux == 0: return []
* s = bam1_aux( src )
* result = [] # <<<<<<<<<<<<<<
* auxtag[2] = 0
* while s < (src.data + src.data_len):
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_result = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2507
+ /* "csamtools.pyx":2507
* s = bam1_aux( src )
* result = []
* auxtag[2] = 0 # <<<<<<<<<<<<<<
*/
(__pyx_v_auxtag[2]) = 0;
- /* "pysam/csamtools.pyx":2508
+ /* "csamtools.pyx":2508
* result = []
* auxtag[2] = 0
* while s < (src.data + src.data_len): # <<<<<<<<<<<<<<
* auxtag[0] = s[0]
*/
while (1) {
- __pyx_t_2 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
- if (!__pyx_t_2) break;
+ __pyx_t_1 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
+ if (!__pyx_t_1) break;
- /* "pysam/csamtools.pyx":2510
+ /* "csamtools.pyx":2510
* while s < (src.data + src.data_len):
* # get tag
* auxtag[0] = s[0] # <<<<<<<<<<<<<<
*/
(__pyx_v_auxtag[0]) = (__pyx_v_s[0]);
- /* "pysam/csamtools.pyx":2511
+ /* "csamtools.pyx":2511
* # get tag
* auxtag[0] = s[0]
* auxtag[1] = s[1] # <<<<<<<<<<<<<<
*/
(__pyx_v_auxtag[1]) = (__pyx_v_s[1]);
- /* "pysam/csamtools.pyx":2512
+ /* "csamtools.pyx":2512
* auxtag[0] = s[0]
* auxtag[1] = s[1]
* s += 2 # <<<<<<<<<<<<<<
*/
__pyx_v_s = (__pyx_v_s + 2);
- /* "pysam/csamtools.pyx":2513
+ /* "csamtools.pyx":2513
* auxtag[1] = s[1]
* s += 2
* auxtype = s[0] # <<<<<<<<<<<<<<
*/
__pyx_v_auxtype = (__pyx_v_s[0]);
- /* "pysam/csamtools.pyx":2514
+ /* "csamtools.pyx":2514
* s += 2
* auxtype = s[0]
* if auxtype in ('c', 'C'): # <<<<<<<<<<<<<<
* value = <int>bam_aux2i(s)
* s += 1
*/
- __pyx_t_4 = __pyx_v_auxtype;
- __pyx_t_2 = ((int)(__pyx_t_4 == 'c'));
- if (!__pyx_t_2) {
- __pyx_t_5 = ((int)(__pyx_t_4 == 'C'));
- __pyx_t_6 = __pyx_t_5;
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 'c'));
+ if (!__pyx_t_1) {
+ __pyx_t_4 = ((int)(__pyx_t_3 == 'C'));
+ __pyx_t_5 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_2;
+ __pyx_t_5 = __pyx_t_1;
}
- __pyx_t_2 = __pyx_t_6;
- if (__pyx_t_2) {
+ __pyx_t_1 = __pyx_t_5;
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2515
+ /* "csamtools.pyx":2515
* auxtype = s[0]
* if auxtype in ('c', 'C'):
* value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype in ('s', 'S'):
*/
- __pyx_t_3 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2516
+ /* "csamtools.pyx":2516
* if auxtype in ('c', 'C'):
* value = <int>bam_aux2i(s)
* s += 1 # <<<<<<<<<<<<<<
* value = <int>bam_aux2i(s)
*/
__pyx_v_s = (__pyx_v_s + 1);
- goto __pyx_L6;
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2517
+ /* "csamtools.pyx":2517
* value = <int>bam_aux2i(s)
* s += 1
* elif auxtype in ('s', 'S'): # <<<<<<<<<<<<<<
* value = <int>bam_aux2i(s)
* s += 2
*/
- __pyx_t_4 = __pyx_v_auxtype;
- __pyx_t_2 = ((int)(__pyx_t_4 == 's'));
- if (!__pyx_t_2) {
- __pyx_t_6 = ((int)(__pyx_t_4 == 'S'));
- __pyx_t_5 = __pyx_t_6;
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 's'));
+ if (!__pyx_t_1) {
+ __pyx_t_5 = ((int)(__pyx_t_3 == 'S'));
+ __pyx_t_4 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_2;
+ __pyx_t_4 = __pyx_t_1;
}
- __pyx_t_2 = __pyx_t_5;
- if (__pyx_t_2) {
+ __pyx_t_1 = __pyx_t_4;
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2518
+ /* "csamtools.pyx":2518
* s += 1
* elif auxtype in ('s', 'S'):
* value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype in ('i', 'I'):
*/
- __pyx_t_3 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2519
+ /* "csamtools.pyx":2519
* elif auxtype in ('s', 'S'):
* value = <int>bam_aux2i(s)
* s += 2 # <<<<<<<<<<<<<<
* value = <int32_t>bam_aux2i(s)
*/
__pyx_v_s = (__pyx_v_s + 2);
- goto __pyx_L6;
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2520
+ /* "csamtools.pyx":2520
* value = <int>bam_aux2i(s)
* s += 2
* elif auxtype in ('i', 'I'): # <<<<<<<<<<<<<<
* value = <int32_t>bam_aux2i(s)
* s += 4
*/
- __pyx_t_4 = __pyx_v_auxtype;
- __pyx_t_2 = ((int)(__pyx_t_4 == 'i'));
- if (!__pyx_t_2) {
- __pyx_t_5 = ((int)(__pyx_t_4 == 'I'));
- __pyx_t_6 = __pyx_t_5;
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 'i'));
+ if (!__pyx_t_1) {
+ __pyx_t_4 = ((int)(__pyx_t_3 == 'I'));
+ __pyx_t_5 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_2;
+ __pyx_t_5 = __pyx_t_1;
}
- __pyx_t_2 = __pyx_t_6;
- if (__pyx_t_2) {
+ __pyx_t_1 = __pyx_t_5;
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2521
+ /* "csamtools.pyx":2521
* s += 2
* elif auxtype in ('i', 'I'):
* value = <int32_t>bam_aux2i(s) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'f':
*/
- __pyx_t_3 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2522
+ /* "csamtools.pyx":2522
* elif auxtype in ('i', 'I'):
* value = <int32_t>bam_aux2i(s)
* s += 4 # <<<<<<<<<<<<<<
* value = <float>bam_aux2f(s)
*/
__pyx_v_s = (__pyx_v_s + 4);
- goto __pyx_L6;
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2523
+ /* "csamtools.pyx":2523
* value = <int32_t>bam_aux2i(s)
* s += 4
* elif auxtype == 'f': # <<<<<<<<<<<<<<
* value = <float>bam_aux2f(s)
* s += 4
*/
- __pyx_t_2 = (__pyx_v_auxtype == 'f');
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_auxtype == 'f');
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2524
+ /* "csamtools.pyx":2524
* s += 4
* elif auxtype == 'f':
* value = <float>bam_aux2f(s) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'd':
*/
- __pyx_t_3 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2525
+ /* "csamtools.pyx":2525
* elif auxtype == 'f':
* value = <float>bam_aux2f(s)
* s += 4 # <<<<<<<<<<<<<<
* value = <double>bam_aux2d(s)
*/
__pyx_v_s = (__pyx_v_s + 4);
- goto __pyx_L6;
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2526
+ /* "csamtools.pyx":2526
* value = <float>bam_aux2f(s)
* s += 4
* elif auxtype == 'd': # <<<<<<<<<<<<<<
* value = <double>bam_aux2d(s)
* s += 8
*/
- __pyx_t_2 = (__pyx_v_auxtype == 'd');
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_auxtype == 'd');
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2527
+ /* "csamtools.pyx":2527
* s += 4
* elif auxtype == 'd':
* value = <double>bam_aux2d(s) # <<<<<<<<<<<<<<
* s += 8
* elif auxtype == 'A':
*/
- __pyx_t_3 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2528
+ /* "csamtools.pyx":2528
* elif auxtype == 'd':
* value = <double>bam_aux2d(s)
* s += 8 # <<<<<<<<<<<<<<
* value = "%c" % <char>bam_aux2A(s)
*/
__pyx_v_s = (__pyx_v_s + 8);
- goto __pyx_L6;
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2529
+ /* "csamtools.pyx":2529
* value = <double>bam_aux2d(s)
* s += 8
* elif auxtype == 'A': # <<<<<<<<<<<<<<
* value = "%c" % <char>bam_aux2A(s)
* s += 1
*/
- __pyx_t_2 = (__pyx_v_auxtype == 'A');
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_auxtype == 'A');
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2530
+ /* "csamtools.pyx":2530
* s += 8
* elif auxtype == 'A':
* value = "%c" % <char>bam_aux2A(s) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype in ('Z', 'H'):
*/
- __pyx_t_3 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), __pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_2 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = ((PyObject *)__pyx_t_7);
- __pyx_t_7 = 0;
+ __pyx_v_value = ((PyObject *)__pyx_t_6);
+ __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":2531
+ /* "csamtools.pyx":2531
* elif auxtype == 'A':
* value = "%c" % <char>bam_aux2A(s)
* s += 1 # <<<<<<<<<<<<<<
* value = _charptr_to_str(<char*>bam_aux2Z(s))
*/
__pyx_v_s = (__pyx_v_s + 1);
- goto __pyx_L6;
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2532
+ /* "csamtools.pyx":2532
* value = "%c" % <char>bam_aux2A(s)
* s += 1
* elif auxtype in ('Z', 'H'): # <<<<<<<<<<<<<<
* value = _charptr_to_str(<char*>bam_aux2Z(s))
* # +1 for NULL terminated string
*/
- __pyx_t_4 = __pyx_v_auxtype;
- __pyx_t_2 = ((int)(__pyx_t_4 == 'Z'));
- if (!__pyx_t_2) {
- __pyx_t_6 = ((int)(__pyx_t_4 == 'H'));
- __pyx_t_5 = __pyx_t_6;
+ __pyx_t_3 = __pyx_v_auxtype;
+ __pyx_t_1 = ((int)(__pyx_t_3 == 'Z'));
+ if (!__pyx_t_1) {
+ __pyx_t_5 = ((int)(__pyx_t_3 == 'H'));
+ __pyx_t_4 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_2;
+ __pyx_t_4 = __pyx_t_1;
}
- __pyx_t_2 = __pyx_t_5;
- if (__pyx_t_2) {
+ __pyx_t_1 = __pyx_t_4;
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2533
+ /* "csamtools.pyx":2533
* s += 1
* elif auxtype in ('Z', 'H'):
* value = _charptr_to_str(<char*>bam_aux2Z(s)) # <<<<<<<<<<<<<<
* # +1 for NULL terminated string
* s += len(value) + 1
*/
- __pyx_t_7 = __pyx_f_5pysam_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_s))); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_s))); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_value = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":2535
+ /* "csamtools.pyx":2535
* value = _charptr_to_str(<char*>bam_aux2Z(s))
* # +1 for NULL terminated string
* s += len(value) + 1 # <<<<<<<<<<<<<<
* elif auxtype == 'B':
* s += 1
*/
- __pyx_t_8 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_s = (__pyx_v_s + (__pyx_t_8 + 1));
- goto __pyx_L6;
+ __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = (__pyx_v_s + (__pyx_t_7 + 1));
+ goto __pyx_L8;
}
- /* "pysam/csamtools.pyx":2536
+ /* "csamtools.pyx":2536
* # +1 for NULL terminated string
* s += len(value) + 1
* elif auxtype == 'B': # <<<<<<<<<<<<<<
* s += 1
* byte_size, nvalues, value = convertBinaryTagToList( s )
*/
- __pyx_t_2 = (__pyx_v_auxtype == 'B');
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_auxtype == 'B');
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2537
+ /* "csamtools.pyx":2537
* s += len(value) + 1
* elif auxtype == 'B':
* s += 1 # <<<<<<<<<<<<<<
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "pysam/csamtools.pyx":2538
+ /* "csamtools.pyx":2538
* elif auxtype == 'B':
* s += 1
* byte_size, nvalues, value = convertBinaryTagToList( s ) # <<<<<<<<<<<<<<
* # 5 for 1 char and 1 int
* s += 5 + ( nvalues * byte_size) - 1
*/
- __pyx_t_7 = __pyx_f_5pysam_9csamtools_convertBinaryTagToList(__pyx_v_s); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
- PyObject* sequence = __pyx_t_7;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 3)) {
- if (size > 3) __Pyx_RaiseTooManyValuesError(3);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = __pyx_f_9csamtools_convertBinaryTagToList(__pyx_v_s); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
+ PyObject* sequence = __pyx_t_6;
if (likely(PyTuple_CheckExact(sequence))) {
- __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
- __pyx_t_10 = PyTuple_GET_ITEM(sequence, 2);
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
+ if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 2);
} else {
- __pyx_t_3 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
- __pyx_t_10 = PyList_GET_ITEM(sequence, 2);
+ if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
+ if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 2);
}
- __Pyx_INCREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_8);
__Pyx_INCREF(__pyx_t_9);
- __Pyx_INCREF(__pyx_t_10);
- #else
- __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- } else
- {
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ } else {
Py_ssize_t index = -1;
- __pyx_t_11 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_3 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_3)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_3);
- index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_9);
- index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L7_unpacking_failed;
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L8_unpacking_done;
- __pyx_L7_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L9_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L9_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_8);
+ index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L9_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ goto __pyx_L10_unpacking_done;
+ __pyx_L9_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L8_unpacking_done:;
+ __pyx_L10_unpacking_done:;
}
- __pyx_t_13 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_3); if (unlikely((__pyx_t_13 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_14 = __Pyx_PyInt_from_py_int32_t(__pyx_t_9); if (unlikely((__pyx_t_14 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_v_byte_size = __pyx_t_13;
- __pyx_v_nvalues = __pyx_t_14;
+ __pyx_t_12 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_2); if (unlikely((__pyx_t_12 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_13 = __Pyx_PyInt_from_py_int32_t(__pyx_t_8); if (unlikely((__pyx_t_13 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_byte_size = __pyx_t_12;
+ __pyx_v_nvalues = __pyx_t_13;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_value = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":2540
+ /* "csamtools.pyx":2540
* byte_size, nvalues, value = convertBinaryTagToList( s )
* # 5 for 1 char and 1 int
* s += 5 + ( nvalues * byte_size) - 1 # <<<<<<<<<<<<<<
* s += 1
*/
__pyx_v_s = (__pyx_v_s + ((5 + (__pyx_v_nvalues * __pyx_v_byte_size)) - 1));
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":2542
+ /* "csamtools.pyx":2542
* s += 5 + ( nvalues * byte_size) - 1
*
* s += 1 # <<<<<<<<<<<<<<
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "pysam/csamtools.pyx":2544
+ /* "csamtools.pyx":2544
* s += 1
*
* result.append( (_charptr_to_str(auxtag), value) ) # <<<<<<<<<<<<<<
*
* return result
*/
- __pyx_t_7 = __pyx_f_5pysam_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_7 = 0;
- __pyx_t_15 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_10)); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_6 = 0;
+ __pyx_t_14 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
}
- /* "pysam/csamtools.pyx":2546
+ /* "csamtools.pyx":2546
* result.append( (_charptr_to_str(auxtag), value) )
*
* return result # <<<<<<<<<<<<<<
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tags.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tags.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tags));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2548
+/* "csamtools.pyx":2548
* return result
*
* def __set__(self, tags): # <<<<<<<<<<<<<<
* cdef uint8_t * s
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags) {
+static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_s;
char *__pyx_v_temp;
PyObject *__pyx_v_buffer = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- PyObject *(*__pyx_t_6)(PyObject *);
+ int __pyx_t_3;
+ Py_ssize_t __pyx_t_4;
+ PyObject *(*__pyx_t_5)(PyObject *);
+ PyObject *__pyx_t_6 = NULL;
PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *(*__pyx_t_10)(PyObject *);
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
int __pyx_t_11;
- int __pyx_t_12;
- Py_ssize_t __pyx_t_13;
+ Py_ssize_t __pyx_t_12;
+ PyObject *__pyx_t_13 = NULL;
PyObject *__pyx_t_14 = NULL;
- PyObject *__pyx_t_15 = NULL;
- int __pyx_t_16;
- size_t __pyx_t_17;
- int __pyx_t_18;
- char *__pyx_t_19;
+ int __pyx_t_15;
+ size_t __pyx_t_16;
+ int __pyx_t_17;
+ char *__pyx_t_18;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2548);
- /* "pysam/csamtools.pyx":2554
+ /* "csamtools.pyx":2554
* cdef char * temp
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* fmts, args = ["<"], []
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2556
+ /* "csamtools.pyx":2556
* src = self._delegate
*
* fmts, args = ["<"], [] # <<<<<<<<<<<<<<
*
* if tags != None:
*/
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_138));
- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_138));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_138));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138));
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_fmts = __pyx_t_2;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_fmts = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __pyx_v_args = __pyx_t_2;
__pyx_t_2 = 0;
- __pyx_v_args = __pyx_t_3;
- __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":2558
+ /* "csamtools.pyx":2558
* fmts, args = ["<"], []
*
* if tags != None: # <<<<<<<<<<<<<<
*
* # map samtools code to python.struct code and byte size
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_tags, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_tags, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":2561
+ /* "csamtools.pyx":2561
*
* # map samtools code to python.struct code and byte size
* for pytag, value in tags: # <<<<<<<<<<<<<<
* pytag = pytag.encode('ascii')
*/
if (PyList_CheckExact(__pyx_v_tags) || PyTuple_CheckExact(__pyx_v_tags)) {
- __pyx_t_3 = __pyx_v_tags; __Pyx_INCREF(__pyx_t_3); __pyx_t_5 = 0;
- __pyx_t_6 = NULL;
+ __pyx_t_2 = __pyx_v_tags; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_5 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_tags); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = Py_TYPE(__pyx_t_3)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_tags); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_5 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_3)) {
- if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_3)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_3)) {
- if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
} else {
- __pyx_t_2 = __pyx_t_6(__pyx_t_3);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_1 = __pyx_t_5(__pyx_t_2);
+ if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_1);
}
- if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
- PyObject* sequence = __pyx_t_2;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
+ if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
+ PyObject* sequence = __pyx_t_1;
if (likely(PyTuple_CheckExact(sequence))) {
- __pyx_t_7 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_8 = PyTuple_GET_ITEM(sequence, 1);
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
} else {
- __pyx_t_7 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_8 = PyList_GET_ITEM(sequence, 1);
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 1);
}
+ __Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
- __Pyx_INCREF(__pyx_t_8);
- #else
- __pyx_t_7 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else
- {
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ } else {
Py_ssize_t index = -1;
- __pyx_t_9 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
- index = 0; __pyx_t_7 = __pyx_t_10(__pyx_t_9); if (unlikely(!__pyx_t_7)) goto __pyx_L6_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_7);
- index = 1; __pyx_t_8 = __pyx_t_10(__pyx_t_9); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_10(__pyx_t_9), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = NULL;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_10 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_6);
+ index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_7);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_pytag);
- __pyx_v_pytag = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_pytag = __pyx_t_6;
+ __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_value = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":2562
+ /* "csamtools.pyx":2562
* # map samtools code to python.struct code and byte size
* for pytag, value in tags:
* if not type(pytag) is bytes: # <<<<<<<<<<<<<<
* pytag = pytag.encode('ascii')
* t = type(value)
*/
- __pyx_t_4 = (((PyObject *)Py_TYPE(__pyx_v_pytag)) == ((PyObject *)((PyObject*)(&PyBytes_Type))));
- __pyx_t_11 = (!__pyx_t_4);
- if (__pyx_t_11) {
+ __pyx_t_3 = (((PyObject *)Py_TYPE(__pyx_v_pytag)) == ((PyObject *)((PyObject*)(&PyBytes_Type))));
+ __pyx_t_10 = (!__pyx_t_3);
+ if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":2563
+ /* "csamtools.pyx":2563
* for pytag, value in tags:
* if not type(pytag) is bytes:
* pytag = pytag.encode('ascii') # <<<<<<<<<<<<<<
* t = type(value)
*
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_pytag, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_pytag, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_v_pytag);
- __pyx_v_pytag = __pyx_t_8;
- __pyx_t_8 = 0;
- goto __pyx_L8;
+ __pyx_v_pytag = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":2564
+ /* "csamtools.pyx":2564
* if not type(pytag) is bytes:
* pytag = pytag.encode('ascii')
* t = type(value) # <<<<<<<<<<<<<<
__Pyx_XDECREF(((PyObject *)__pyx_v_t));
__pyx_v_t = ((PyObject*)((PyObject *)Py_TYPE(__pyx_v_value)));
- /* "pysam/csamtools.pyx":2566
+ /* "csamtools.pyx":2566
* t = type(value)
*
* if t is tuple or t is list: # <<<<<<<<<<<<<<
* # binary tags - treat separately
* pytype = 'B'
*/
- __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyTuple_Type)));
- if (!__pyx_t_11) {
- __pyx_t_4 = (__pyx_v_t == ((PyObject*)(&PyList_Type)));
- __pyx_t_12 = __pyx_t_4;
+ __pyx_t_10 = (__pyx_v_t == ((PyObject*)(&PyTuple_Type)));
+ if (!__pyx_t_10) {
+ __pyx_t_3 = (__pyx_v_t == ((PyObject*)(&PyList_Type)));
+ __pyx_t_11 = __pyx_t_3;
} else {
- __pyx_t_12 = __pyx_t_11;
+ __pyx_t_11 = __pyx_t_10;
}
- if (__pyx_t_12) {
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2568
+ /* "csamtools.pyx":2568
* if t is tuple or t is list:
* # binary tags - treat separately
* pytype = 'B' # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = ((PyObject *)__pyx_n_s__B);
- /* "pysam/csamtools.pyx":2570
+ /* "csamtools.pyx":2570
* pytype = 'B'
* # get data type - first value determines type
* if type(value[0]) is float: # <<<<<<<<<<<<<<
* datafmt, datatype = "f", "f"
* else:
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_value, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_12 = (((PyObject *)Py_TYPE(__pyx_t_8)) == ((PyObject *)((PyObject*)(&PyFloat_Type))));
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_12) {
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_value, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = (((PyObject *)Py_TYPE(__pyx_t_7)) == ((PyObject *)((PyObject*)(&PyFloat_Type))));
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2571
+ /* "csamtools.pyx":2571
* # get data type - first value determines type
* if type(value[0]) is float:
* datafmt, datatype = "f", "f" # <<<<<<<<<<<<<<
* else:
* mi, ma = min(value), max(value)
*/
- __pyx_t_8 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_2 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_datafmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L10;
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L12;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2573
+ /* "csamtools.pyx":2573
* datafmt, datatype = "f", "f"
* else:
* mi, ma = min(value), max(value) # <<<<<<<<<<<<<<
* absmax = max( abs(mi), abs(ma) )
* # signed ints
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_7 = PyObject_Call(__pyx_builtin_max, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_max, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_mi);
- __pyx_v_mi = __pyx_t_8;
- __pyx_t_8 = 0;
- __Pyx_XDECREF(__pyx_v_ma);
- __pyx_v_ma = __pyx_t_7;
+ __pyx_v_mi = __pyx_t_7;
__pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_ma);
+ __pyx_v_ma = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":2574
+ /* "csamtools.pyx":2574
* else:
* mi, ma = min(value), max(value)
* absmax = max( abs(mi), abs(ma) ) # <<<<<<<<<<<<<<
* # signed ints
* if mi < 0:
*/
- __pyx_t_7 = PyNumber_Absolute(__pyx_v_ma); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Absolute(__pyx_v_ma); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyNumber_Absolute(__pyx_v_mi); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyNumber_Absolute(__pyx_v_mi); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_6, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_7, __pyx_t_8, Py_GT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- if (__pyx_t_12) {
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_2 = __pyx_t_7;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_11) {
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = __pyx_t_6;
} else {
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_2 = __pyx_t_8;
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_1 = __pyx_t_7;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = __pyx_t_2;
- __Pyx_INCREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_absmax);
- __pyx_v_absmax = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_absmax = __pyx_t_1;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2576
+ /* "csamtools.pyx":2576
* absmax = max( abs(mi), abs(ma) )
* # signed ints
* if mi < 0: # <<<<<<<<<<<<<<
* if mi >= -127: datafmt, datatype = "b", 'c'
* elif mi >= -32767: datafmt, datatype = "h", 's'
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_12) {
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2577
+ /* "csamtools.pyx":2577
* # signed ints
* if mi < 0:
* if mi >= -127: datafmt, datatype = "b", 'c' # <<<<<<<<<<<<<<
* elif mi >= -32767: datafmt, datatype = "h", 's'
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_127, Py_GE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_12) {
- __pyx_t_7 = ((PyObject *)__pyx_n_s__b);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_2 = ((PyObject *)__pyx_n_s__c);
- __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__b);
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__c);
+ __Pyx_INCREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_datafmt = __pyx_t_1;
+ __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L12;
+ __pyx_v_datatype = __pyx_t_6;
+ __pyx_t_6 = 0;
+ goto __pyx_L14;
}
- /* "pysam/csamtools.pyx":2578
+ /* "csamtools.pyx":2578
* if mi < 0:
* if mi >= -127: datafmt, datatype = "b", 'c'
* elif mi >= -32767: datafmt, datatype = "h", 's' # <<<<<<<<<<<<<<
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "i", 'i'
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_32767, Py_GE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_12) {
- __pyx_t_2 = ((PyObject *)__pyx_n_s__h);
- __Pyx_INCREF(__pyx_t_2);
- __pyx_t_7 = ((PyObject *)__pyx_n_s__s);
- __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__h);
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__s);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_datafmt = __pyx_t_6;
+ __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L12;
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L14;
}
- /* "pysam/csamtools.pyx":2579
+ /* "csamtools.pyx":2579
* if mi >= -127: datafmt, datatype = "b", 'c'
* elif mi >= -32767: datafmt, datatype = "h", 's'
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: datafmt, datatype = "i", 'i'
*
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_neg_2147483648, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_12) {
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L12;
+ goto __pyx_L14;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2580
+ /* "csamtools.pyx":2580
* elif mi >= -32767: datafmt, datatype = "h", 's'
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "i", 'i' # <<<<<<<<<<<<<<
*
* # unsigned ints
*/
- __pyx_t_7 = ((PyObject *)__pyx_n_s__i);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_2 = ((PyObject *)__pyx_n_s__i);
- __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_datafmt = __pyx_t_1;
+ __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_datatype = __pyx_t_6;
+ __pyx_t_6 = 0;
}
- __pyx_L12:;
- goto __pyx_L11;
+ __pyx_L14:;
+ goto __pyx_L13;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2584
+ /* "csamtools.pyx":2584
* # unsigned ints
* else:
* if absmax <= 255: datafmt, datatype = "B", 'C' # <<<<<<<<<<<<<<
* elif absmax <= 65535: datafmt, datatype = "H", 'S'
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_255, Py_LE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_12) {
- __pyx_t_2 = ((PyObject *)__pyx_n_s__B);
- __Pyx_INCREF(__pyx_t_2);
- __pyx_t_7 = ((PyObject *)__pyx_n_s__C);
- __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__B);
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__C);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_datafmt = __pyx_t_6;
+ __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L13;
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L15;
}
- /* "pysam/csamtools.pyx":2585
+ /* "csamtools.pyx":2585
* else:
* if absmax <= 255: datafmt, datatype = "B", 'C'
* elif absmax <= 65535: datafmt, datatype = "H", 'S' # <<<<<<<<<<<<<<
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "I", 'I'
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_65535, Py_LE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_12) {
- __pyx_t_7 = ((PyObject *)__pyx_n_s__H);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_2 = ((PyObject *)__pyx_n_s__S);
- __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__H);
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__S);
+ __Pyx_INCREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_datafmt = __pyx_t_1;
+ __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_2;
- __pyx_t_2 = 0;
- goto __pyx_L13;
+ __pyx_v_datatype = __pyx_t_6;
+ __pyx_t_6 = 0;
+ goto __pyx_L15;
}
- /* "pysam/csamtools.pyx":2586
+ /* "csamtools.pyx":2586
* if absmax <= 255: datafmt, datatype = "B", 'C'
* elif absmax <= 65535: datafmt, datatype = "H", 'S'
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: datafmt, datatype = "I", 'I'
*
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_4294967295, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_12) {
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_Raise(__pyx_t_6, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L13;
+ goto __pyx_L15;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2587
+ /* "csamtools.pyx":2587
* elif absmax <= 65535: datafmt, datatype = "H", 'S'
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "I", 'I' # <<<<<<<<<<<<<<
*
* datafmt = "2sccI%i%s" % (len(value), datafmt)
*/
- __pyx_t_2 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_2);
- __pyx_t_7 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_6 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_1 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_datafmt = __pyx_t_6;
+ __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_datatype = __pyx_t_1;
+ __pyx_t_1 = 0;
}
- __pyx_L13:;
+ __pyx_L15:;
}
- __pyx_L11:;
+ __pyx_L13:;
}
- __pyx_L10:;
+ __pyx_L12:;
- /* "pysam/csamtools.pyx":2589
+ /* "csamtools.pyx":2589
* else: datafmt, datatype = "I", 'I'
*
* datafmt = "2sccI%i%s" % (len(value), datafmt) # <<<<<<<<<<<<<<
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
*/
- __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_datafmt);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_datafmt);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_datafmt);
__Pyx_GIVEREF(__pyx_v_datafmt);
- __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_141), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_141), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = ((PyObject *)__pyx_t_7);
- __pyx_t_7 = 0;
+ __pyx_v_datafmt = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2590
+ /* "csamtools.pyx":2590
*
* datafmt = "2sccI%i%s" % (len(value), datafmt)
* args.extend( [pytag[:2], # <<<<<<<<<<<<<<
* pytype.encode('ascii'),
* datatype.encode('ascii'),
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":2593
+ /* "csamtools.pyx":2593
* pytype.encode('ascii'),
* datatype.encode('ascii'),
* len(value)] + list(value) ) # <<<<<<<<<<<<<<
* fmts.append( datafmt )
* continue
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
- /* "pysam/csamtools.pyx":2591
+ /* "csamtools.pyx":2591
* datafmt = "2sccI%i%s" % (len(value), datafmt)
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* datatype.encode('ascii'),
* len(value)] + list(value) )
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_142), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_142), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":2592
+ /* "csamtools.pyx":2592
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
* datatype.encode('ascii'), # <<<<<<<<<<<<<<
* len(value)] + list(value) )
* fmts.append( datafmt )
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_datatype, __pyx_n_s__encode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_14 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_143), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_datatype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_13 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_143), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":2593
+ /* "csamtools.pyx":2593
* pytype.encode('ascii'),
* datatype.encode('ascii'),
* len(value)] + list(value) ) # <<<<<<<<<<<<<<
* fmts.append( datafmt )
* continue
*/
- __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = PyList_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- PyList_SET_ITEM(__pyx_t_15, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- PyList_SET_ITEM(__pyx_t_15, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- PyList_SET_ITEM(__pyx_t_15, 2, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- PyList_SET_ITEM(__pyx_t_15, 3, __pyx_t_8);
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_14 = PyList_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ PyList_SET_ITEM(__pyx_t_14, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ PyList_SET_ITEM(__pyx_t_14, 1, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_2 = 0;
- __pyx_t_9 = 0;
- __pyx_t_14 = 0;
+ PyList_SET_ITEM(__pyx_t_14, 2, __pyx_t_13);
+ __Pyx_GIVEREF(__pyx_t_13);
+ PyList_SET_ITEM(__pyx_t_14, 3, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_6 = 0;
__pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_13 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Add(((PyObject *)__pyx_t_15), __pyx_t_14); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Add(((PyObject *)__pyx_t_14), __pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":2594
+ /* "csamtools.pyx":2594
* datatype.encode('ascii'),
* len(value)] + list(value) )
* fmts.append( datafmt ) # <<<<<<<<<<<<<<
* continue
*
*/
- __pyx_t_16 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_16 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2595
+ /* "csamtools.pyx":2595
* len(value)] + list(value) )
* fmts.append( datafmt )
* continue # <<<<<<<<<<<<<<
*
* if t is float:
*/
- goto __pyx_L4_continue;
- goto __pyx_L9;
+ goto __pyx_L6_continue;
+ goto __pyx_L11;
}
- __pyx_L9:;
+ __pyx_L11:;
- /* "pysam/csamtools.pyx":2597
+ /* "csamtools.pyx":2597
* continue
*
* if t is float: # <<<<<<<<<<<<<<
* fmt, pytype = "2scf", 'f'
* elif t is int:
*/
- __pyx_t_12 = (__pyx_v_t == ((PyObject*)(&PyFloat_Type)));
- if (__pyx_t_12) {
+ __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyFloat_Type)));
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2598
+ /* "csamtools.pyx":2598
*
* if t is float:
* fmt, pytype = "2scf", 'f' # <<<<<<<<<<<<<<
* elif t is int:
* # negative values
*/
- __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scf);
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_14 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scf);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_14;
- __pyx_t_14 = 0;
- goto __pyx_L14;
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L16;
}
- /* "pysam/csamtools.pyx":2599
+ /* "csamtools.pyx":2599
* if t is float:
* fmt, pytype = "2scf", 'f'
* elif t is int: # <<<<<<<<<<<<<<
* # negative values
* if value < 0:
*/
- __pyx_t_12 = (__pyx_v_t == ((PyObject*)(&PyInt_Type)));
- if (__pyx_t_12) {
+ __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyInt_Type)));
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2601
+ /* "csamtools.pyx":2601
* elif t is int:
* # negative values
* if value < 0: # <<<<<<<<<<<<<<
* if value >= -127: fmt, pytype = "2scb", 'c'
* elif value >= -32767: fmt, pytype = "2sch", 's'
*/
- __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- if (__pyx_t_12) {
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2602
+ /* "csamtools.pyx":2602
* # negative values
* if value < 0:
* if value >= -127: fmt, pytype = "2scb", 'c' # <<<<<<<<<<<<<<
* elif value >= -32767: fmt, pytype = "2sch", 's'
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_127, Py_GE); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- if (__pyx_t_12) {
- __pyx_t_14 = ((PyObject *)__pyx_kp_s__2scb);
- __Pyx_INCREF(__pyx_t_14);
- __pyx_t_8 = ((PyObject *)__pyx_n_s__c);
- __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_13 = ((PyObject *)__pyx_kp_s__2scb);
+ __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__c);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_14;
- __pyx_t_14 = 0;
+ __pyx_v_fmt = __pyx_t_13;
+ __pyx_t_13 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_8;
- __pyx_t_8 = 0;
- goto __pyx_L16;
+ __pyx_v_pytype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L18;
}
- /* "pysam/csamtools.pyx":2603
+ /* "csamtools.pyx":2603
* if value < 0:
* if value >= -127: fmt, pytype = "2scb", 'c'
* elif value >= -32767: fmt, pytype = "2sch", 's' # <<<<<<<<<<<<<<
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2sci", 'i'
*/
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_32767, Py_GE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_12) {
- __pyx_t_8 = ((PyObject *)__pyx_kp_s__2sch);
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_14 = ((PyObject *)__pyx_n_s__s);
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2sch);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__s);
+ __Pyx_INCREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_14;
- __pyx_t_14 = 0;
- goto __pyx_L16;
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L18;
}
- /* "pysam/csamtools.pyx":2604
+ /* "csamtools.pyx":2604
* if value >= -127: fmt, pytype = "2scb", 'c'
* elif value >= -32767: fmt, pytype = "2sch", 's'
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: fmt, pytype = "2sci", 'i'
* # positive values
*/
- __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_2147483648, Py_LT); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- if (__pyx_t_12) {
- __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_14));
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_14));
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_14, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_13));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_13));
+ __pyx_t_13 = 0;
+ __pyx_t_13 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_13, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ goto __pyx_L18;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2605
+ /* "csamtools.pyx":2605
* elif value >= -32767: fmt, pytype = "2sch", 's'
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2sci", 'i' # <<<<<<<<<<<<<<
* # positive values
* else:
*/
- __pyx_t_14 = ((PyObject *)__pyx_kp_s__2sci);
- __Pyx_INCREF(__pyx_t_14);
- __pyx_t_8 = ((PyObject *)__pyx_n_s__i);
- __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_13 = ((PyObject *)__pyx_kp_s__2sci);
+ __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_14;
- __pyx_t_14 = 0;
+ __pyx_v_fmt = __pyx_t_13;
+ __pyx_t_13 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_pytype = __pyx_t_7;
+ __pyx_t_7 = 0;
}
- __pyx_L16:;
- goto __pyx_L15;
+ __pyx_L18:;
+ goto __pyx_L17;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2608
+ /* "csamtools.pyx":2608
* # positive values
* else:
* if value <= 255: fmt, pytype = "2scB", 'C' # <<<<<<<<<<<<<<
* elif value <= 65535: fmt, pytype = "2scH", 'S'
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_value, __pyx_int_255, Py_LE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_12) {
- __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scB);
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_14 = ((PyObject *)__pyx_n_s__C);
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scB);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__C);
+ __Pyx_INCREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_14;
- __pyx_t_14 = 0;
- goto __pyx_L17;
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L19;
}
- /* "pysam/csamtools.pyx":2609
+ /* "csamtools.pyx":2609
* else:
* if value <= 255: fmt, pytype = "2scB", 'C'
* elif value <= 65535: fmt, pytype = "2scH", 'S' # <<<<<<<<<<<<<<
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2scI", 'I'
*/
- __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_65535, Py_LE); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- if (__pyx_t_12) {
- __pyx_t_14 = ((PyObject *)__pyx_kp_s__2scH);
- __Pyx_INCREF(__pyx_t_14);
- __pyx_t_8 = ((PyObject *)__pyx_n_s__S);
- __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_13 = ((PyObject *)__pyx_kp_s__2scH);
+ __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__S);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_14;
- __pyx_t_14 = 0;
+ __pyx_v_fmt = __pyx_t_13;
+ __pyx_t_13 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_8;
- __pyx_t_8 = 0;
- goto __pyx_L17;
+ __pyx_v_pytype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L19;
}
- /* "pysam/csamtools.pyx":2610
+ /* "csamtools.pyx":2610
* if value <= 255: fmt, pytype = "2scB", 'C'
* elif value <= 65535: fmt, pytype = "2scH", 'S'
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: fmt, pytype = "2scI", 'I'
* else:
*/
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_value, __pyx_int_4294967295, Py_GT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_12) {
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L17;
+ goto __pyx_L19;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2611
+ /* "csamtools.pyx":2611
* elif value <= 65535: fmt, pytype = "2scH", 'S'
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2scI", 'I' # <<<<<<<<<<<<<<
* else:
* # Note: hex strings (H) are not supported yet
*/
- __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scI);
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_14 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scI);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_14;
- __pyx_t_14 = 0;
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
}
- __pyx_L17:;
+ __pyx_L19:;
}
- __pyx_L15:;
- goto __pyx_L14;
+ __pyx_L17:;
+ goto __pyx_L16;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2614
+ /* "csamtools.pyx":2614
* else:
* # Note: hex strings (H) are not supported yet
* if t is not bytes: # <<<<<<<<<<<<<<
* value = value.encode('ascii')
* if len(value) == 1:
*/
- __pyx_t_12 = (__pyx_v_t != ((PyObject*)(&PyBytes_Type)));
- if (__pyx_t_12) {
+ __pyx_t_11 = (__pyx_v_t != ((PyObject*)(&PyBytes_Type)));
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2615
+ /* "csamtools.pyx":2615
* # Note: hex strings (H) are not supported yet
* if t is not bytes:
* value = value.encode('ascii') # <<<<<<<<<<<<<<
* if len(value) == 1:
* fmt, pytype = "2scc", 'A'
*/
- __pyx_t_14 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__encode); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_8 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_k_tuple_144), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_13 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__encode); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_7 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_k_tuple_144), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_8;
- __pyx_t_8 = 0;
- goto __pyx_L18;
+ __pyx_v_value = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L20;
}
- __pyx_L18:;
+ __pyx_L20:;
- /* "pysam/csamtools.pyx":2616
+ /* "csamtools.pyx":2616
* if t is not bytes:
* value = value.encode('ascii')
* if len(value) == 1: # <<<<<<<<<<<<<<
* fmt, pytype = "2scc", 'A'
* else:
*/
- __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = (__pyx_t_13 == 1);
- if (__pyx_t_12) {
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = (__pyx_t_12 == 1);
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2617
+ /* "csamtools.pyx":2617
* value = value.encode('ascii')
* if len(value) == 1:
* fmt, pytype = "2scc", 'A' # <<<<<<<<<<<<<<
* else:
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
*/
- __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scc);
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_14 = ((PyObject *)__pyx_n_s__A);
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scc);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__A);
+ __Pyx_INCREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_fmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_14;
- __pyx_t_14 = 0;
- goto __pyx_L19;
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
+ goto __pyx_L21;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2619
+ /* "csamtools.pyx":2619
* fmt, pytype = "2scc", 'A'
* else:
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z' # <<<<<<<<<<<<<<
*
* args.extend( [pytag[:2],
*/
- __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_145), __pyx_t_14); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_14 = ((PyObject *)__pyx_n_s__Z);
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyInt_FromSsize_t((__pyx_t_12 + 1)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_145), __pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __pyx_t_13 = ((PyObject *)__pyx_n_s__Z);
+ __Pyx_INCREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = ((PyObject *)__pyx_t_8);
- __pyx_t_8 = 0;
+ __pyx_v_fmt = ((PyObject *)__pyx_t_7);
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_14;
- __pyx_t_14 = 0;
+ __pyx_v_pytype = __pyx_t_13;
+ __pyx_t_13 = 0;
}
- __pyx_L19:;
+ __pyx_L21:;
}
- __pyx_L14:;
+ __pyx_L16:;
- /* "pysam/csamtools.pyx":2621
+ /* "csamtools.pyx":2621
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
*
* args.extend( [pytag[:2], # <<<<<<<<<<<<<<
* pytype.encode('ascii'),
* value ] )
*/
- __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_13 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
- /* "pysam/csamtools.pyx":2622
+ /* "csamtools.pyx":2622
*
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* value ] )
*
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_15 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_146), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_146), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2623
+ /* "csamtools.pyx":2623
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
* value ] ) # <<<<<<<<<<<<<<
*
* fmts.append( fmt )
*/
- __pyx_t_7 = PyList_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- PyList_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- PyList_SET_ITEM(__pyx_t_7, 1, __pyx_t_15);
- __Pyx_GIVEREF(__pyx_t_15);
+ __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
__Pyx_INCREF(__pyx_v_value);
- PyList_SET_ITEM(__pyx_t_7, 2, __pyx_v_value);
+ PyList_SET_ITEM(__pyx_t_1, 2, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_8 = 0;
- __pyx_t_15 = 0;
- __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_1));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2625
+ /* "csamtools.pyx":2625
* value ] )
*
* fmts.append( fmt ) # <<<<<<<<<<<<<<
*
* fmt = "".join(fmts)
*/
- __pyx_t_16 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_16 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L4_continue:;
+ if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L6_continue:;
}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2627
+ /* "csamtools.pyx":2627
* fmts.append( fmt )
*
* fmt = "".join(fmts) # <<<<<<<<<<<<<<
* total_size = struct.calcsize(fmt)
* buffer = ctypes.create_string_buffer(total_size)
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_v_fmts));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_fmts));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fmts));
__Pyx_GIVEREF(((PyObject *)__pyx_v_fmts));
- __pyx_t_15 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_15;
- __pyx_t_15 = 0;
+ __pyx_v_fmt = __pyx_t_14;
+ __pyx_t_14 = 0;
- /* "pysam/csamtools.pyx":2628
+ /* "csamtools.pyx":2628
*
* fmt = "".join(fmts)
* total_size = struct.calcsize(fmt) # <<<<<<<<<<<<<<
* buffer = ctypes.create_string_buffer(total_size)
* struct.pack_into( fmt,
*/
- __pyx_t_15 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_15, __pyx_n_s__calcsize); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_14 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_14, __pyx_n_s__calcsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
__Pyx_INCREF(__pyx_v_fmt);
- PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_fmt);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_fmt);
__Pyx_GIVEREF(__pyx_v_fmt);
- __pyx_t_3 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
- __pyx_v_total_size = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __pyx_v_total_size = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2629
+ /* "csamtools.pyx":2629
* fmt = "".join(fmts)
* total_size = struct.calcsize(fmt)
* buffer = ctypes.create_string_buffer(total_size) # <<<<<<<<<<<<<<
* struct.pack_into( fmt,
* buffer,
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__ctypes); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s_147); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__ctypes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_14 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s_147); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_total_size);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_total_size);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_total_size);
__Pyx_GIVEREF(__pyx_v_total_size);
- __pyx_t_7 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_v_buffer = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_v_buffer = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2630
+ /* "csamtools.pyx":2630
* total_size = struct.calcsize(fmt)
* buffer = ctypes.create_string_buffer(total_size)
* struct.pack_into( fmt, # <<<<<<<<<<<<<<
* buffer,
* 0,
*/
- __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__pack_into); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__pack_into); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2631
+ /* "csamtools.pyx":2631
* buffer = ctypes.create_string_buffer(total_size)
* struct.pack_into( fmt,
* buffer, # <<<<<<<<<<<<<<
* 0,
* *args )
*/
- __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fmt);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_fmt);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fmt);
__Pyx_GIVEREF(__pyx_v_fmt);
__Pyx_INCREF(__pyx_v_buffer);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_buffer);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_buffer);
__Pyx_GIVEREF(__pyx_v_buffer);
__Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- /* "pysam/csamtools.pyx":2633
+ /* "csamtools.pyx":2633
* buffer,
* 0,
* *args ) # <<<<<<<<<<<<<<
*
* # delete the old data and allocate new space.
*/
- __pyx_t_15 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_15));
- __pyx_t_14 = PyNumber_Add(((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_14));
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
- __pyx_t_15 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_13 = PyNumber_Add(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L3;
+ __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ goto __pyx_L5;
}
- __pyx_L3:;
-
- /* "pysam/csamtools.pyx":2640
- * pysam_bam_update( src,
- * src.l_aux,
- * total_size, # <<<<<<<<<<<<<<
- * bam1_aux( src ) )
- *
- */
- if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5:;
+ if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2641
+ /* "csamtools.pyx":2641
* src.l_aux,
* total_size,
* bam1_aux( src ) ) # <<<<<<<<<<<<<<
*
* src.l_aux = total_size
*/
- pysam_bam_update(__pyx_v_src, __pyx_v_src->l_aux, __pyx_t_17, bam1_aux(__pyx_v_src));
+ pysam_bam_update(__pyx_v_src, __pyx_v_src->l_aux, __pyx_t_16, bam1_aux(__pyx_v_src));
- /* "pysam/csamtools.pyx":2643
+ /* "csamtools.pyx":2643
* bam1_aux( src ) )
*
* src.l_aux = total_size # <<<<<<<<<<<<<<
*
* # copy data only if there is any
*/
- __pyx_t_18 = __Pyx_PyInt_AsInt(__pyx_v_total_size); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_src->l_aux = __pyx_t_18;
+ __pyx_t_17 = __Pyx_PyInt_AsInt(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_src->l_aux = __pyx_t_17;
- /* "pysam/csamtools.pyx":2646
+ /* "csamtools.pyx":2646
*
* # copy data only if there is any
* if total_size != 0: # <<<<<<<<<<<<<<
*
* # get location of new data
*/
- __pyx_t_15 = PyObject_RichCompare(__pyx_v_total_size, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_15); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_15); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (__pyx_t_12) {
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_total_size, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":2649
+ /* "csamtools.pyx":2649
*
* # get location of new data
* s = bam1_aux( src ) # <<<<<<<<<<<<<<
* # check if there is direct path from buffer.raw to tmp
*/
__pyx_v_s = bam1_aux(__pyx_v_src);
+ if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_14 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2652
+ /* "csamtools.pyx":2652
*
* # check if there is direct path from buffer.raw to tmp
* temp = buffer.raw # <<<<<<<<<<<<<<
* memcpy( s, temp, total_size )
*
*/
- if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_15 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __pyx_t_19 = PyBytes_AsString(__pyx_t_15); if (unlikely((!__pyx_t_19) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __pyx_v_temp = __pyx_t_19;
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_18 = PyBytes_AsString(__pyx_t_14); if (unlikely((!__pyx_t_18) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_v_temp = __pyx_t_18;
- /* "pysam/csamtools.pyx":2653
+ /* "csamtools.pyx":2653
* # check if there is direct path from buffer.raw to tmp
* temp = buffer.raw
* memcpy( s, temp, total_size ) # <<<<<<<<<<<<<<
*
* property flag:
*/
- __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- memcpy(__pyx_v_s, __pyx_v_temp, __pyx_t_17);
- goto __pyx_L20;
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ memcpy(__pyx_v_s, __pyx_v_temp, __pyx_t_16);
+ goto __pyx_L22;
}
- __pyx_L20:;
+ __pyx_L22:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_13);
__Pyx_XDECREF(__pyx_t_14);
- __Pyx_XDECREF(__pyx_t_15);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tags.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tags.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_fmts);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2657
+/* "csamtools.pyx":2657
* property flag:
* """properties flag"""
* def __get__(self): return self._delegate.core.flag # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2657);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.flag.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.flag.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_flag));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2658
+/* "csamtools.pyx":2658
* """properties flag"""
* def __get__(self): return self._delegate.core.flag
* def __set__(self, flag): self._delegate.core.flag = flag # <<<<<<<<<<<<<<
* property rname:
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag) {
+static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2658);
__pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_flag); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.flag = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.flag.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.flag.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2676
+/* "csamtools.pyx":2676
*
* """
* def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2676);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.rname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2677
+/* "csamtools.pyx":2677
* """
* def __get__(self): return self._delegate.core.tid
* def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
* property tid:
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
+static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2677);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.tid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.rname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2690
+/* "csamtools.pyx":2690
*
* """
* def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2690);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2691
+/* "csamtools.pyx":2691
* """
* def __get__(self): return self._delegate.core.tid
* def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
* property pos:
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
+static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2691);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.tid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tid.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tid.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2695
+/* "csamtools.pyx":2695
* property pos:
* """0-based leftmost coordinate"""
* def __get__(self): return self._delegate.core.pos # <<<<<<<<<<<<<<
* ## setting the cigar string also updates the "bin" attribute
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2695);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_pos));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2696
+/* "csamtools.pyx":2696
* """0-based leftmost coordinate"""
* def __get__(self): return self._delegate.core.pos
* def __set__(self, pos): # <<<<<<<<<<<<<<
* cdef bam1_t * src
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos) {
+static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
bam1_t *__pyx_v_src;
int __pyx_r;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int32_t __pyx_t_2;
+ int32_t __pyx_t_1;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2696);
- /* "pysam/csamtools.pyx":2699
+ /* "csamtools.pyx":2699
* ## setting the cigar string also updates the "bin" attribute
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar:
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2700
+ /* "csamtools.pyx":2700
* cdef bam1_t * src
* src = self._delegate
* if src.core.n_cigar: # <<<<<<<<<<<<<<
*/
if (__pyx_v_src->core.n_cigar) {
- /* "pysam/csamtools.pyx":2701
+ /* "csamtools.pyx":2701
* src = self._delegate
* if src.core.n_cigar:
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) ) # <<<<<<<<<<<<<<
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
*/
__pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)));
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2703
+ /* "csamtools.pyx":2703
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
* else:
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1) # <<<<<<<<<<<<<<
*/
__pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, (__pyx_v_src->core.pos + 1));
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2704
+ /* "csamtools.pyx":2704
* else:
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
* self._delegate.core.pos = pos # <<<<<<<<<<<<<<
* property bin:
* """properties bin"""
*/
- __pyx_t_2 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_2 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.pos = __pyx_t_2;
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.pos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2707
+/* "csamtools.pyx":2707
* property bin:
* """properties bin"""
* def __get__(self): return self._delegate.core.bin # <<<<<<<<<<<<<<
* property rlen:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2707);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.bin.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.bin.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_bin));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2708
+/* "csamtools.pyx":2708
* """properties bin"""
* def __get__(self): return self._delegate.core.bin
* def __set__(self, bin): self._delegate.core.bin = bin # <<<<<<<<<<<<<<
* '''length of the read (read only). Returns 0 if not given.'''
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin) {
+static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2708);
__pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_bin); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.bin = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.bin.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.bin.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2711
+/* "csamtools.pyx":2711
* property rlen:
* '''length of the read (read only). Returns 0 if not given.'''
* def __get__(self): return self._delegate.core.l_qseq # <<<<<<<<<<<<<<
* '''aligned reference position of the read on the reference genome.
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2711);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.rlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2717
+/* "csamtools.pyx":2717
* aend points to one past the last aligned residue.
* Returns None if not available.'''
* def __get__(self): # <<<<<<<<<<<<<<
* src = self._delegate
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- int __pyx_t_6;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2717);
- /* "pysam/csamtools.pyx":2719
+ /* "csamtools.pyx":2719
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2720
+ /* "csamtools.pyx":2720
* cdef bam1_t * src
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
* return None
* return bam_calend(&src.core, bam1_cigar(src))
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_And(__pyx_t_2, __pyx_int_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_4) {
- __pyx_t_5 = (__pyx_v_src->core.n_cigar == 0);
- __pyx_t_6 = __pyx_t_5;
+ if (!__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
+ __pyx_t_5 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_4;
+ __pyx_t_5 = __pyx_t_3;
}
- if (__pyx_t_6) {
+ if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2721
+ /* "csamtools.pyx":2721
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None # <<<<<<<<<<<<<<
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2722
+ /* "csamtools.pyx":2722
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
* return bam_calend(&src.core, bam1_cigar(src)) # <<<<<<<<<<<<<<
* property alen:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.aend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.aend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2727
+/* "csamtools.pyx":2727
* '''aligned length of the read on the reference genome. Returns None if
* not available.'''
* def __get__(self): # <<<<<<<<<<<<<<
* src = self._delegate
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- int __pyx_t_6;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2727);
- /* "pysam/csamtools.pyx":2729
+ /* "csamtools.pyx":2729
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2730
+ /* "csamtools.pyx":2730
* cdef bam1_t * src
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
* return None
* return bam_calend(&src.core,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_And(__pyx_t_2, __pyx_int_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_4) {
- __pyx_t_5 = (__pyx_v_src->core.n_cigar == 0);
- __pyx_t_6 = __pyx_t_5;
+ if (!__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
+ __pyx_t_5 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_4;
+ __pyx_t_5 = __pyx_t_3;
}
- if (__pyx_t_6) {
+ if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2731
+ /* "csamtools.pyx":2731
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None # <<<<<<<<<<<<<<
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2732
+ /* "csamtools.pyx":2732
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
* return bam_calend(&src.core, # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
- /* "pysam/csamtools.pyx":2734
+ /* "csamtools.pyx":2734
* return bam_calend(&src.core,
* bam1_cigar(src)) - \
* self._delegate.core.pos # <<<<<<<<<<<<<<
*
* property mapq:
*/
- __pyx_t_3 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - __pyx_v_self->_delegate->core.pos)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.alen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.alen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2738
+/* "csamtools.pyx":2738
* property mapq:
* """mapping quality"""
* def __get__(self): return self._delegate.core.qual # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2738);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mapq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2739
+/* "csamtools.pyx":2739
* """mapping quality"""
* def __get__(self): return self._delegate.core.qual
* def __set__(self, qual): self._delegate.core.qual = qual # <<<<<<<<<<<<<<
* property mrnm:
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
+static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2739);
__pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.qual = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mapq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2745
+/* "csamtools.pyx":2745
* deprecated, use RNEXT instead.
* """
* def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
* property rnext:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2745);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mrnm.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2746
+/* "csamtools.pyx":2746
* """
* def __get__(self): return self._delegate.core.mtid
* def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
* """the :term:`reference` id of the mate """
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2746);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mrnm.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2749
+/* "csamtools.pyx":2749
* property rnext:
* """the :term:`reference` id of the mate """
* def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
* property mpos:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2749);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.rnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2750
+/* "csamtools.pyx":2750
* """the :term:`reference` id of the mate """
* def __get__(self): return self._delegate.core.mtid
* def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
* """the position of the mate
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2750);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.rnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2754
+/* "csamtools.pyx":2754
* """the position of the mate
* deprecated, use PNEXT instead."""
* def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
* property pnext:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2754);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2755
+/* "csamtools.pyx":2755
* deprecated, use PNEXT instead."""
* def __get__(self): return self._delegate.core.mpos
* def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
* """the position of the mate"""
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2755);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mpos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2758
+/* "csamtools.pyx":2758
* property pnext:
* """the position of the mate"""
* def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
* property isize:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2758);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.pnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2759
+/* "csamtools.pyx":2759
* """the position of the mate"""
* def __get__(self): return self._delegate.core.mpos
* def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
* """the insert size
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2759);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.pnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2763
+/* "csamtools.pyx":2763
* """the insert size
* deprecated: use tlen instead"""
* def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
* property tlen:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2763);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.isize.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.isize.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2764
+/* "csamtools.pyx":2764
* deprecated: use tlen instead"""
* def __get__(self): return self._delegate.core.isize
* def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
* """the insert size"""
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
+static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2764);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.isize = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.isize.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.isize.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2767
+/* "csamtools.pyx":2767
* property tlen:
* """the insert size"""
* def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
* property is_paired:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2767);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2768
+/* "csamtools.pyx":2768
* """the insert size"""
* def __get__(self): return self._delegate.core.isize
* def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
* """true if read is paired in sequencing"""
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
+static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2768);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.isize = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tlen.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.tlen.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2771
+/* "csamtools.pyx":2771
* property is_paired:
* """true if read is paired in sequencing"""
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FPAIRED
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2771);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(((__pyx_v_self->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(((((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_paired.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2772
+/* "csamtools.pyx":2772
* """true if read is paired in sequencing"""
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FPAIRED
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2772);
- /* "pysam/csamtools.pyx":2773
+ /* "csamtools.pyx":2773
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPAIRED # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2774
+ /* "csamtools.pyx":2774
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPAIRED
* else: self._delegate.core.flag &= ~BAM_FPAIRED # <<<<<<<<<<<<<<
* property is_proper_pair:
* """true if read is mapped in a proper pair"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_paired.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2777
+/* "csamtools.pyx":2777
* property is_proper_pair:
* """true if read is mapped in a proper pair"""
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2777);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_proper_pair.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2778
+/* "csamtools.pyx":2778
* """true if read is mapped in a proper pair"""
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2778);
- /* "pysam/csamtools.pyx":2779
+ /* "csamtools.pyx":2779
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 2);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 2);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2780
+ /* "csamtools.pyx":2780
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
* else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
* property is_unmapped:
* """true if read itself is unmapped"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~2));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~2));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_proper_pair.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2783
+/* "csamtools.pyx":2783
* property is_unmapped:
* """true if read itself is unmapped"""
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FUNMAP
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2783);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2784
+/* "csamtools.pyx":2784
* """true if read itself is unmapped"""
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FUNMAP
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2784);
- /* "pysam/csamtools.pyx":2785
+ /* "csamtools.pyx":2785
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FUNMAP # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 4);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 4);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2786
+ /* "csamtools.pyx":2786
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FUNMAP
* else: self._delegate.core.flag &= ~BAM_FUNMAP # <<<<<<<<<<<<<<
* property mate_is_unmapped:
* """true if the mate is unmapped"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~4));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~4));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2789
+/* "csamtools.pyx":2789
* property mate_is_unmapped:
* """true if the mate is unmapped"""
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FMUNMAP
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2789);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2790
+/* "csamtools.pyx":2790
* """true if the mate is unmapped"""
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FMUNMAP
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2790);
- /* "pysam/csamtools.pyx":2791
+ /* "csamtools.pyx":2791
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMUNMAP # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 8);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 8);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2792
+ /* "csamtools.pyx":2792
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMUNMAP
* else: self._delegate.core.flag &= ~BAM_FMUNMAP # <<<<<<<<<<<<<<
* property is_reverse:
* """true if read is mapped to reverse strand"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~8));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~8));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2795
+/* "csamtools.pyx":2795
* property is_reverse:
* """true if read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FREVERSE
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2795);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2796
+/* "csamtools.pyx":2796
* """true if read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FREVERSE
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2796);
- /* "pysam/csamtools.pyx":2797
+ /* "csamtools.pyx":2797
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREVERSE # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 16);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 16);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2798
+ /* "csamtools.pyx":2798
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREVERSE
* else: self._delegate.core.flag &= ~BAM_FREVERSE # <<<<<<<<<<<<<<
* property mate_is_reverse:
* """true is read is mapped to reverse strand"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~16));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~16));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2801
+/* "csamtools.pyx":2801
* property mate_is_reverse:
* """true is read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FMREVERSE
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2801);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2802
+/* "csamtools.pyx":2802
* """true is read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FMREVERSE
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2802);
- /* "pysam/csamtools.pyx":2803
+ /* "csamtools.pyx":2803
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMREVERSE # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 32);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 32);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2804
+ /* "csamtools.pyx":2804
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMREVERSE
* else: self._delegate.core.flag &= ~BAM_FMREVERSE # <<<<<<<<<<<<<<
* property is_read1:
* """true if this is read1"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~32));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~32));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2807
+/* "csamtools.pyx":2807
* property is_read1:
* """true if this is read1"""
* def __get__(self): return (self.flag & BAM_FREAD1) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FREAD1
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2807);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_64); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read1.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2808
+/* "csamtools.pyx":2808
* """true if this is read1"""
* def __get__(self): return (self.flag & BAM_FREAD1) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FREAD1
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2808);
- /* "pysam/csamtools.pyx":2809
+ /* "csamtools.pyx":2809
* def __get__(self): return (self.flag & BAM_FREAD1) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD1 # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 64);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 64);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2810
+ /* "csamtools.pyx":2810
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD1
* else: self._delegate.core.flag &= ~BAM_FREAD1 # <<<<<<<<<<<<<<
* property is_read2:
* """true if this is read2"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~64));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~64));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read1.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2813
+/* "csamtools.pyx":2813
* property is_read2:
* """true if this is read2"""
* def __get__(self): return (self.flag & BAM_FREAD2) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FREAD2
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2813);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_128); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read2.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2814
+/* "csamtools.pyx":2814
* """true if this is read2"""
* def __get__(self): return (self.flag & BAM_FREAD2) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FREAD2
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2814);
- /* "pysam/csamtools.pyx":2815
+ /* "csamtools.pyx":2815
* def __get__(self): return (self.flag & BAM_FREAD2) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD2 # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 128);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 128);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2816
+ /* "csamtools.pyx":2816
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD2
* else: self._delegate.core.flag &= ~BAM_FREAD2 # <<<<<<<<<<<<<<
* property is_secondary:
* """true if not primary alignment"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~128));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~128));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read2.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2819
+/* "csamtools.pyx":2819
* property is_secondary:
* """true if not primary alignment"""
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FSECONDARY
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2819);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_256); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_secondary.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2820
+/* "csamtools.pyx":2820
* """true if not primary alignment"""
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FSECONDARY
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2820);
- /* "pysam/csamtools.pyx":2821
+ /* "csamtools.pyx":2821
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FSECONDARY # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 256);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 256);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2822
+ /* "csamtools.pyx":2822
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FSECONDARY
* else: self._delegate.core.flag &= ~BAM_FSECONDARY # <<<<<<<<<<<<<<
* property is_qcfail:
* """true if QC failure"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~256));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~256));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_secondary.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2825
+/* "csamtools.pyx":2825
* property is_qcfail:
* """true if QC failure"""
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FQCFAIL
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2825);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_512); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_qcfail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2826
+/* "csamtools.pyx":2826
* """true if QC failure"""
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FQCFAIL
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2826);
- /* "pysam/csamtools.pyx":2827
+ /* "csamtools.pyx":2827
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FQCFAIL # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 512);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 512);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2828
+ /* "csamtools.pyx":2828
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FQCFAIL
* else: self._delegate.core.flag &= ~BAM_FQCFAIL # <<<<<<<<<<<<<<
* property is_duplicate:
* """true if optical or PCR duplicate"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~512));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~512));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_qcfail.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2831
+/* "csamtools.pyx":2831
* property is_duplicate:
* """true if optical or PCR duplicate"""
* def __get__(self): return (self.flag & BAM_FDUP) != 0 # <<<<<<<<<<<<<<
* if val: self._delegate.core.flag |= BAM_FDUP
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2831);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_1024); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_duplicate.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2832
+/* "csamtools.pyx":2832
* """true if optical or PCR duplicate"""
* def __get__(self): return (self.flag & BAM_FDUP) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FDUP
*/
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2832);
- /* "pysam/csamtools.pyx":2833
+ /* "csamtools.pyx":2833
* def __get__(self): return (self.flag & BAM_FDUP) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FDUP # <<<<<<<<<<<<<<
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1024);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1024);
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2834
+ /* "csamtools.pyx":2834
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FDUP
* else: self._delegate.core.flag &= ~BAM_FDUP # <<<<<<<<<<<<<<
* property positions:
* """a list of reference positions that this read aligns to."""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1024));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1024));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_duplicate.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2837
+/* "csamtools.pyx":2837
* property positions:
* """a list of reference positions that this read aligns to."""
* def __get__(self): # <<<<<<<<<<<<<<
* cdef int op
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self) {
uint32_t __pyx_v_k;
uint32_t __pyx_v_i;
uint32_t __pyx_v_pos;
PyObject *__pyx_v_l = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- int32_t __pyx_t_4;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ uint32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
uint32_t __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- uint32_t __pyx_t_7;
- int __pyx_t_8;
+ int __pyx_t_6;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2837);
- /* "pysam/csamtools.pyx":2843
+ /* "csamtools.pyx":2843
* cdef bam1_t * src
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return []
*
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2844
+ /* "csamtools.pyx":2844
*
* src = self._delegate
* if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
*
* result = []
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2846
+ /* "csamtools.pyx":2846
* if src.core.n_cigar == 0: return []
*
* result = [] # <<<<<<<<<<<<<<
* pos = src.core.pos
* cigar_p = bam1_cigar(src)
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_result = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2847
+ /* "csamtools.pyx":2847
*
* result = []
* pos = src.core.pos # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src)
*
*/
- __pyx_t_4 = __pyx_v_src->core.pos;
- __pyx_v_pos = __pyx_t_4;
+ __pyx_v_pos = __pyx_v_src->core.pos;
- /* "pysam/csamtools.pyx":2848
+ /* "csamtools.pyx":2848
* result = []
* pos = src.core.pos
* cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2850
+ /* "csamtools.pyx":2850
* cigar_p = bam1_cigar(src)
*
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_5 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
+ __pyx_t_3 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2851
+ /* "csamtools.pyx":2851
*
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2852
+ /* "csamtools.pyx":2852
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l:
*/
- __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_l = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2853
+ /* "csamtools.pyx":2853
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* if op == BAM_CMATCH: # <<<<<<<<<<<<<<
* for i from pos <= i < pos + l:
* result.append( i )
*/
- __pyx_t_2 = (__pyx_v_op == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_op == 0);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2854
+ /* "csamtools.pyx":2854
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( i )
*
*/
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "pysam/csamtools.pyx":2855
+ /* "csamtools.pyx":2855
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l:
* result.append( i ) # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyList_Append(__pyx_v_result, __pyx_t_6); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = PyList_Append(__pyx_v_result, __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
- /* "pysam/csamtools.pyx":2857
+ /* "csamtools.pyx":2857
* result.append( i )
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
case 2:
case 3:
- /* "pysam/csamtools.pyx":2858
+ /* "csamtools.pyx":2858
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
* pos += l # <<<<<<<<<<<<<<
*
* return result
*/
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_3); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_pos = __pyx_t_7;
+ __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_2); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_pos = __pyx_t_5;
break;
}
}
- /* "pysam/csamtools.pyx":2860
+ /* "csamtools.pyx":2860
* pos += l
*
* return result # <<<<<<<<<<<<<<
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.positions.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools.AlignedRead.positions.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2867
+/* "csamtools.pyx":2867
* Unaligned position are marked by None.
* """
* def __get__(self): # <<<<<<<<<<<<<<
* cdef int op
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self) {
uint32_t __pyx_v_k;
uint32_t __pyx_v_i;
uint32_t __pyx_v_pos;
PyObject *__pyx_v_l = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- int32_t __pyx_t_4;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ uint32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
uint32_t __pyx_t_5;
PyObject *__pyx_t_6 = NULL;
- uint32_t __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
+ int __pyx_t_7;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2867);
- /* "pysam/csamtools.pyx":2873
+ /* "csamtools.pyx":2873
* cdef bam1_t * src
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return []
*
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2874
+ /* "csamtools.pyx":2874
*
* src = self._delegate
* if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
*
* result = []
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2876
+ /* "csamtools.pyx":2876
* if src.core.n_cigar == 0: return []
*
* result = [] # <<<<<<<<<<<<<<
* pos = src.core.pos
* qpos = 0
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_result = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_v_result = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2877
+ /* "csamtools.pyx":2877
*
* result = []
* pos = src.core.pos # <<<<<<<<<<<<<<
* qpos = 0
* cigar_p = bam1_cigar(src)
*/
- __pyx_t_4 = __pyx_v_src->core.pos;
- __pyx_v_pos = __pyx_t_4;
+ __pyx_v_pos = __pyx_v_src->core.pos;
- /* "pysam/csamtools.pyx":2878
+ /* "csamtools.pyx":2878
* result = []
* pos = src.core.pos
* qpos = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_qpos = 0;
- /* "pysam/csamtools.pyx":2879
+ /* "csamtools.pyx":2879
* pos = src.core.pos
* qpos = 0
* cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2881
+ /* "csamtools.pyx":2881
* cigar_p = bam1_cigar(src)
*
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_5 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
+ __pyx_t_3 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2882
+ /* "csamtools.pyx":2882
*
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2883
+ /* "csamtools.pyx":2883
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH:
*/
- __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_l = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2896
+ /* "csamtools.pyx":2896
* qpos += 1
*
* elif op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2885
+ /* "csamtools.pyx":2885
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
* if op == BAM_CMATCH: # <<<<<<<<<<<<<<
*/
case 0:
- /* "pysam/csamtools.pyx":2886
+ /* "csamtools.pyx":2886
*
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( (qpos, i) )
* qpos += 1
*/
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "pysam/csamtools.pyx":2887
+ /* "csamtools.pyx":2887
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l:
* result.append( (qpos, i) ) # <<<<<<<<<<<<<<
* qpos += 1
* pos += l
*/
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_6 = 0;
- __pyx_t_3 = 0;
- __pyx_t_9 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_8)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_4 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":2888
+ /* "csamtools.pyx":2888
* for i from pos <= i < pos + l:
* result.append( (qpos, i) )
* qpos += 1 # <<<<<<<<<<<<<<
__pyx_v_qpos = (__pyx_v_qpos + 1);
}
- /* "pysam/csamtools.pyx":2889
+ /* "csamtools.pyx":2889
* result.append( (qpos, i) )
* qpos += 1
* pos += l # <<<<<<<<<<<<<<
*
* elif op == BAM_CINS:
*/
- __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_t_8, __pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_3); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_pos = __pyx_t_7;
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_2); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_pos = __pyx_t_5;
break;
- /* "pysam/csamtools.pyx":2891
+ /* "csamtools.pyx":2891
* pos += l
*
* elif op == BAM_CINS: # <<<<<<<<<<<<<<
*/
case 1:
- /* "pysam/csamtools.pyx":2892
+ /* "csamtools.pyx":2892
*
* elif op == BAM_CINS:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( (qpos, None) )
* qpos += 1
*/
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "pysam/csamtools.pyx":2893
+ /* "csamtools.pyx":2893
* elif op == BAM_CINS:
* for i from pos <= i < pos + l:
* result.append( (qpos, None) ) # <<<<<<<<<<<<<<
* qpos += 1
*
*/
- __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_t_3, 1, Py_None);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, Py_None);
__Pyx_GIVEREF(Py_None);
- __pyx_t_8 = 0;
- __pyx_t_9 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_3)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_6 = 0;
+ __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2894
+ /* "csamtools.pyx":2894
* for i from pos <= i < pos + l:
* result.append( (qpos, None) )
* qpos += 1 # <<<<<<<<<<<<<<
}
break;
- /* "pysam/csamtools.pyx":2896
+ /* "csamtools.pyx":2896
* qpos += 1
*
* elif op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
case 2:
case 3:
- /* "pysam/csamtools.pyx":2897
+ /* "csamtools.pyx":2897
*
* elif op == BAM_CDEL or op == BAM_CREF_SKIP:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( (None, i) )
* pos += l
*/
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
- /* "pysam/csamtools.pyx":2898
+ /* "csamtools.pyx":2898
* elif op == BAM_CDEL or op == BAM_CREF_SKIP:
* for i from pos <= i < pos + l:
* result.append( (None, i) ) # <<<<<<<<<<<<<<
* pos += l
*
*/
- __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_t_3, 0, Py_None);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, Py_None);
__Pyx_GIVEREF(Py_None);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_8 = 0;
- __pyx_t_9 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_3)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
}
- /* "pysam/csamtools.pyx":2899
+ /* "csamtools.pyx":2899
* for i from pos <= i < pos + l:
* result.append( (None, i) )
* pos += l # <<<<<<<<<<<<<<
*
* return result
*/
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = PyNumber_InPlaceAdd(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_v_pos = __pyx_t_7;
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyNumber_InPlaceAdd(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_v_pos = __pyx_t_5;
break;
}
}
- /* "pysam/csamtools.pyx":2901
+ /* "csamtools.pyx":2901
* pos += l
*
* return result # <<<<<<<<<<<<<<
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.aligned_pairs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.aligned_pairs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11AlignedRead_10overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":2904
+ *
+ *
+ * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
+ * """return number of aligned bases of read overlapping the interval *start* and *end*
+ * on the reference sequence.
+ */
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_5overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
- PyObject *__pyx_r = 0;
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_pos;
+ uint32_t __pyx_v_overlap;
+ int __pyx_v_op;
+ int __pyx_v_o;
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_l = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("overlap (wrapper)", 0);
+ int __pyx_t_1;
+ uint32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ uint32_t __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ uint32_t __pyx_t_8;
+ uint32_t __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("overlap");
+ __Pyx_TraceCall("overlap", __pyx_f[0], 2904);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), __pyx_v_start, __pyx_v_end);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-/* "pysam/csamtools.pyx":2904
- *
- *
- * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
- * """return number of aligned bases of read overlapping the interval *start* and *end*
- * on the reference sequence.
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_pos;
- uint32_t __pyx_v_overlap;
- int __pyx_v_op;
- int __pyx_v_o;
- uint32_t *__pyx_v_cigar_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_l = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- bam1_t *__pyx_t_1;
- int __pyx_t_2;
- int32_t __pyx_t_3;
- uint32_t __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- uint32_t __pyx_t_6;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- uint32_t __pyx_t_10;
- uint32_t __pyx_t_11;
- int __pyx_t_12;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("overlap", 0);
- __Pyx_TraceCall("overlap", __pyx_f[0], 2904);
-
- /* "pysam/csamtools.pyx":2913
+ /* "csamtools.pyx":2913
* cdef bam1_t * src
*
* overlap = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_overlap = 0;
- /* "pysam/csamtools.pyx":2915
+ /* "csamtools.pyx":2915
* overlap = 0
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos
*/
- __pyx_t_1 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_1;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
- /* "pysam/csamtools.pyx":2916
+ /* "csamtools.pyx":2916
*
* src = self._delegate
* if src.core.n_cigar == 0: return 0 # <<<<<<<<<<<<<<
* pos = src.core.pos
* o = 0
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(__pyx_int_0);
__pyx_r = __pyx_int_0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":2917
+ /* "csamtools.pyx":2917
* src = self._delegate
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos # <<<<<<<<<<<<<<
* o = 0
*
*/
- __pyx_t_3 = __pyx_v_src->core.pos;
- __pyx_v_pos = __pyx_t_3;
+ __pyx_v_pos = __pyx_v_src->core.pos;
- /* "pysam/csamtools.pyx":2918
+ /* "csamtools.pyx":2918
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos
* o = 0 # <<<<<<<<<<<<<<
*/
__pyx_v_o = 0;
- /* "pysam/csamtools.pyx":2920
+ /* "csamtools.pyx":2920
* o = 0
*
* cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2921
+ /* "csamtools.pyx":2921
*
* cigar_p = bam1_cigar(src)
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_4 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
+ __pyx_t_2 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_2; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2922
+ /* "csamtools.pyx":2922
* cigar_p = bam1_cigar(src)
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2923
+ /* "csamtools.pyx":2923
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH:
*/
- __pyx_t_5 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_l = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":2925
+ /* "csamtools.pyx":2925
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
* if op == BAM_CMATCH: # <<<<<<<<<<<<<<
* o = min( pos + l, end) - max( pos, start )
* if o > 0: overlap += o
*/
- __pyx_t_2 = (__pyx_v_op == 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_op == 0);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2926
+ /* "csamtools.pyx":2926
*
* if op == BAM_CMATCH:
* o = min( pos + l, end) - max( pos, start ) # <<<<<<<<<<<<<<
* if o > 0: overlap += o
*
*/
- __pyx_t_6 = __pyx_v_end;
- __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_v_end;
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyNumber_Add(__pyx_t_5, __pyx_v_l); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_t_7, Py_LT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- if (__pyx_t_2) {
- __pyx_t_9 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_6); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_5 = __pyx_t_9;
- __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_1) {
+ __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_3 = __pyx_t_7;
+ __pyx_t_7 = 0;
} else {
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_5 = __pyx_t_7;
+ __Pyx_INCREF(__pyx_t_5);
+ __pyx_t_3 = __pyx_t_5;
}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_6 = __pyx_v_start;
- __pyx_t_10 = __pyx_v_pos;
- if ((__pyx_t_6 > __pyx_t_10)) {
- __pyx_t_11 = __pyx_t_6;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __pyx_v_start;
+ __pyx_t_8 = __pyx_v_pos;
+ if ((__pyx_t_4 > __pyx_t_8)) {
+ __pyx_t_9 = __pyx_t_4;
} else {
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_9 = __pyx_t_8;
}
- __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_11); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyNumber_Subtract(__pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = PyNumber_Subtract(__pyx_t_5, __pyx_t_7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_v_o = __pyx_t_12;
+ __pyx_v_o = __pyx_t_10;
- /* "pysam/csamtools.pyx":2927
+ /* "csamtools.pyx":2927
* if op == BAM_CMATCH:
* o = min( pos + l, end) - max( pos, start )
* if o > 0: overlap += o # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
- __pyx_t_2 = (__pyx_v_o > 0);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_o > 0);
+ if (__pyx_t_1) {
__pyx_v_overlap = (__pyx_v_overlap + __pyx_v_o);
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
- goto __pyx_L6;
+ __pyx_L10:;
+ goto __pyx_L9;
}
- __pyx_L6:;
+ __pyx_L9:;
- /* "pysam/csamtools.pyx":2929
+ /* "csamtools.pyx":2929
* if o > 0: overlap += o
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
case 2:
case 3:
- /* "pysam/csamtools.pyx":2930
+ /* "csamtools.pyx":2930
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
* pos += l # <<<<<<<<<<<<<<
*
* return overlap
*/
- __pyx_t_9 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_t_9, __pyx_v_l); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_11 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_7); if (unlikely((__pyx_t_11 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_7, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_v_pos = __pyx_t_11;
+ __pyx_t_9 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_9 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_v_pos = __pyx_t_9;
break;
}
}
- /* "pysam/csamtools.pyx":2932
+ /* "csamtools.pyx":2932
* pos += l
*
* return overlap # <<<<<<<<<<<<<<
* def opt(self, tag):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_overlap); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_overlap); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_r = __pyx_t_5;
+ __pyx_t_5 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_l);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11AlignedRead_12opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("opt (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tag));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2934
+/* "csamtools.pyx":2934
* return overlap
*
* def opt(self, tag): # <<<<<<<<<<<<<<
* #see bam_aux.c: bam_aux_get() and bam_aux2i() etc
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_6opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
uint8_t *__pyx_v_v;
- CYTHON_UNUSED int __pyx_v_nvalues;
+ int __pyx_v_nvalues;
PyObject *__pyx_v_btag = NULL;
PyObject *__pyx_v_auxtype = NULL;
- CYTHON_UNUSED PyObject *__pyx_v_bytesize = NULL;
+ PyObject *__pyx_v_bytesize = NULL;
PyObject *__pyx_v_values = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("opt", 0);
+ __Pyx_RefNannySetupContext("opt");
__Pyx_TraceCall("opt", __pyx_f[0], 2934);
- /* "pysam/csamtools.pyx":2939
+ /* "csamtools.pyx":2939
* cdef uint8_t * v
* cdef int nvalues
* btag = _force_bytes(tag) # <<<<<<<<<<<<<<
* v = bam_aux_get(self._delegate, btag)
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_tag)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_tag)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_btag = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2940
+ /* "csamtools.pyx":2940
* cdef int nvalues
* btag = _force_bytes(tag)
* v = bam_aux_get(self._delegate, btag) # <<<<<<<<<<<<<<
* auxtype = chr(v[0])
*/
__pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_btag)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_v = bam_aux_get(__pyx_v_self->_delegate, __pyx_t_2);
+ __pyx_v_v = bam_aux_get(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate, __pyx_t_2);
- /* "pysam/csamtools.pyx":2941
+ /* "csamtools.pyx":2941
* btag = _force_bytes(tag)
* v = bam_aux_get(self._delegate, btag)
* if v == NULL: raise KeyError( "tag '%s' not present" % tag ) # <<<<<<<<<<<<<<
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_148), __pyx_v_tag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":2942
+ /* "csamtools.pyx":2942
* v = bam_aux_get(self._delegate, btag)
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
* auxtype = chr(v[0]) # <<<<<<<<<<<<<<
__pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__pyx_v_auxtype = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2943
+ /* "csamtools.pyx":2943
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
* auxtype = chr(v[0])
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S': # <<<<<<<<<<<<<<
* return <int>bam_aux2i(v)
* elif auxtype == 'i' or auxtype == 'I':
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__c), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__c), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!__pyx_t_3) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__C), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__C), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!__pyx_t_5) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__s), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__s), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!__pyx_t_6) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__S), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_7 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__S), Py_EQ); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_8 = __pyx_t_7;
} else {
__pyx_t_8 = __pyx_t_6;
}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2944
+ /* "csamtools.pyx":2944
* auxtype = chr(v[0])
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
* return <int>bam_aux2i(v) # <<<<<<<<<<<<<<
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":2945
+ /* "csamtools.pyx":2945
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
* return <int>bam_aux2i(v)
* elif auxtype == 'i' or auxtype == 'I': # <<<<<<<<<<<<<<
* return <int32_t>bam_aux2i(v)
* elif auxtype == 'f' or auxtype == 'F':
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__i), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__i), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!__pyx_t_5) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__I), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__I), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = __pyx_t_3;
} else {
__pyx_t_6 = __pyx_t_5;
}
if (__pyx_t_6) {
- /* "pysam/csamtools.pyx":2946
+ /* "csamtools.pyx":2946
* return <int>bam_aux2i(v)
* elif auxtype == 'i' or auxtype == 'I':
* return <int32_t>bam_aux2i(v) # <<<<<<<<<<<<<<
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":2947
+ /* "csamtools.pyx":2947
* elif auxtype == 'i' or auxtype == 'I':
* return <int32_t>bam_aux2i(v)
* elif auxtype == 'f' or auxtype == 'F': # <<<<<<<<<<<<<<
* return <float>bam_aux2f(v)
* elif auxtype == 'd' or auxtype == 'D':
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__f), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__f), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!__pyx_t_6) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__F), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__F), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __pyx_t_5;
} else {
__pyx_t_3 = __pyx_t_6;
}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":2948
+ /* "csamtools.pyx":2948
* return <int32_t>bam_aux2i(v)
* elif auxtype == 'f' or auxtype == 'F':
* return <float>bam_aux2f(v) # <<<<<<<<<<<<<<
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":2949
+ /* "csamtools.pyx":2949
* elif auxtype == 'f' or auxtype == 'F':
* return <float>bam_aux2f(v)
* elif auxtype == 'd' or auxtype == 'D': # <<<<<<<<<<<<<<
* return <double>bam_aux2d(v)
* elif auxtype == 'A':
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__d), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__d), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!__pyx_t_3) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__D), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__D), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = __pyx_t_6;
} else {
__pyx_t_5 = __pyx_t_3;
}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2950
+ /* "csamtools.pyx":2950
* return <float>bam_aux2f(v)
* elif auxtype == 'd' or auxtype == 'D':
* return <double>bam_aux2d(v) # <<<<<<<<<<<<<<
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":2951
+ /* "csamtools.pyx":2951
* elif auxtype == 'd' or auxtype == 'D':
* return <double>bam_aux2d(v)
* elif auxtype == 'A': # <<<<<<<<<<<<<<
* # there might a more efficient way
* # to convert a char into a string
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__A), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2954
+ /* "csamtools.pyx":2954
* # there might a more efficient way
* # to convert a char into a string
* return '%c' % <char>bam_aux2A(v) # <<<<<<<<<<<<<<
__pyx_r = ((PyObject *)__pyx_t_4);
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":2955
+ /* "csamtools.pyx":2955
* # to convert a char into a string
* return '%c' % <char>bam_aux2A(v)
* elif auxtype == 'Z': # <<<<<<<<<<<<<<
* return _charptr_to_str(<char*>bam_aux2Z(v))
* elif auxtype == 'B':
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__Z), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__Z), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2956
+ /* "csamtools.pyx":2956
* return '%c' % <char>bam_aux2A(v)
* elif auxtype == 'Z':
* return _charptr_to_str(<char*>bam_aux2Z(v)) # <<<<<<<<<<<<<<
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_5pysam_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_v))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_v))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- /* "pysam/csamtools.pyx":2957
+ /* "csamtools.pyx":2957
* elif auxtype == 'Z':
* return _charptr_to_str(<char*>bam_aux2Z(v))
* elif auxtype == 'B': # <<<<<<<<<<<<<<
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
* return values
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__B), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__B), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2958
+ /* "csamtools.pyx":2958
* return _charptr_to_str(<char*>bam_aux2Z(v))
* elif auxtype == 'B':
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 ) # <<<<<<<<<<<<<<
* return values
* else:
*/
- __pyx_t_4 = __pyx_f_5pysam_9csamtools_convertBinaryTagToList((__pyx_v_v + 1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_9csamtools_convertBinaryTagToList((__pyx_v_v + 1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 3)) {
- if (size > 3) __Pyx_RaiseTooManyValuesError(3);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
+ if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 2);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
+ if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_9 = PyList_GET_ITEM(sequence, 1);
__pyx_t_10 = PyList_GET_ITEM(sequence, 2);
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_10);
- #else
- __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_11 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L5_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L5_unpacking_failed;
+ index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L6_unpacking_done;
- __pyx_L5_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L6_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_values = __pyx_t_10;
__pyx_t_10 = 0;
- /* "pysam/csamtools.pyx":2959
+ /* "csamtools.pyx":2959
* elif auxtype == 'B':
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
* return values # <<<<<<<<<<<<<<
__Pyx_INCREF(__pyx_v_values);
__pyx_r = __pyx_v_values;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2961
+ /* "csamtools.pyx":2961
* return values
* else:
* raise ValueError("unknown auxilliary type '%s'" % auxtype) # <<<<<<<<<<<<<<
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_149), __pyx_v_auxtype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L4:;
+ __pyx_L6:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.opt", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.opt", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_btag);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_11AlignedRead_14fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
-static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("fancy_str (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":2964
+/* "csamtools.pyx":2964
*
*
* def fancy_str (self): # <<<<<<<<<<<<<<
* """
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_7fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_v_ret_string = NULL;
PyObject *__pyx_v_field_names = NULL;
PyObject *__pyx_v_fields_names_in_order = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fancy_str", 0);
+ __Pyx_RefNannySetupContext("fancy_str");
__Pyx_TraceCall("fancy_str", __pyx_f[0], 2964);
- /* "pysam/csamtools.pyx":2967
+ /* "csamtools.pyx":2967
* """returns list of fieldnames/values in pretty format for debugging
* """
* ret_string = [] # <<<<<<<<<<<<<<
* "tid": "Contig index",
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_ret_string = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2968
+ /* "csamtools.pyx":2968
* """
* ret_string = []
* field_names = { # <<<<<<<<<<<<<<
__pyx_v_field_names = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2988
+ /* "csamtools.pyx":2988
* "data_len": "Current data length",
* }
* fields_names_in_order = ["tid", "pos", "mtid", "mpos", "isize", "flag", # <<<<<<<<<<<<<<
* "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
*/
__pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_n_s__tid));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tid));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__tid));
__pyx_v_fields_names_in_order = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2992
+ /* "csamtools.pyx":2992
* "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
*
* for f in fields_names_in_order: # <<<<<<<<<<<<<<
* if not f in self.__dict__:
* continue
*/
+ if (unlikely(((PyObject *)__pyx_v_fields_names_in_order) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = ((PyObject *)__pyx_v_fields_names_in_order); __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
__Pyx_XDECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":2993
+ /* "csamtools.pyx":2993
*
* for f in fields_names_in_order:
* if not f in self.__dict__: # <<<<<<<<<<<<<<
* continue
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_3, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((PySequence_Contains(__pyx_t_3, __pyx_v_f))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_5 = (!__pyx_t_4);
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":2994
+ /* "csamtools.pyx":2994
* for f in fields_names_in_order:
* if not f in self.__dict__:
* continue # <<<<<<<<<<<<<<
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*
*/
- goto __pyx_L3_continue;
- goto __pyx_L5;
+ goto __pyx_L5_continue;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":2995
+ /* "csamtools.pyx":2995
* if not f in self.__dict__:
* continue
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f))) # <<<<<<<<<<<<<<
*
* for f in self.__dict__:
*/
+ if (unlikely(((PyObject *)__pyx_v_ret_string) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_field_names), __pyx_v_f); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_kp_s_169), __pyx_v_f); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = PyNumber_Add(__pyx_t_6, ((PyObject *)__pyx_kp_s_170)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_L3_continue:;
+ __pyx_L5_continue:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2997
+ /* "csamtools.pyx":2997
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*
* for f in self.__dict__: # <<<<<<<<<<<<<<
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_9 = __pyx_t_1; __Pyx_INCREF(__pyx_t_9); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_9)) {
+ if (PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_9)) {
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
+ } else if (PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
} else {
__pyx_t_1 = __pyx_t_11(__pyx_t_9);
if (unlikely(!__pyx_t_1)) {
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2998
+ /* "csamtools.pyx":2998
*
* for f in self.__dict__:
* if not f in field_names: # <<<<<<<<<<<<<<
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
* return ret_string
*/
- __pyx_t_5 = (__Pyx_PyDict_Contains(__pyx_v_f, ((PyObject *)__pyx_v_field_names), Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_field_names) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (!__pyx_t_5);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2999
+ /* "csamtools.pyx":2999
* for f in self.__dict__:
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f))) # <<<<<<<<<<<<<<
* return ret_string
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_ret_string) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L8;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/csamtools.pyx":3000
+ /* "csamtools.pyx":3000
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
* return ret_string # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("pysam.csamtools.AlignedRead.fancy_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.AlignedRead.fancy_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_ret_string);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3019
+/* "csamtools.pyx":3019
* will change.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
+static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 3019);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- /* "pysam/csamtools.pyx":3020
+ /* "csamtools.pyx":3020
* '''
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3022
+/* "csamtools.pyx":3022
* raise TypeError("This class cannot be instantiated from Python")
*
* def __str__(self): # <<<<<<<<<<<<<<
* "\n" +\
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 3022);
- /* "pysam/csamtools.pyx":3023
+ /* "csamtools.pyx":3023
*
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
*/
__Pyx_XDECREF(__pyx_r);
- /* "pysam/csamtools.pyx":3024
+ /* "csamtools.pyx":3024
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" +\ # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":3023
+ /* "csamtools.pyx":3023
*
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
* "\n" +\
* "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":3025
+ /* "csamtools.pyx":3025
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" +\
* "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
*/
__pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3029
+/* "csamtools.pyx":3029
* property tid:
* '''the chromosome ID as is defined in the header'''
* def __get__(self): return self.tid # <<<<<<<<<<<<<<
* property n:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3029);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3033
+/* "csamtools.pyx":3033
* property n:
* '''number of reads mapping to this column.'''
* def __get__(self): return self.n_pu # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3033);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.n.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.n.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self), ((PyObject *)__pyx_v_n));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3034
+/* "csamtools.pyx":3034
* '''number of reads mapping to this column.'''
* def __get__(self): return self.n_pu
* def __set__(self, n): self.n_pu = n # <<<<<<<<<<<<<<
* property pos:
*/
-static int __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n) {
+static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
+static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 3034);
__pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_n); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->n_pu = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.n.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.n.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3037
+/* "csamtools.pyx":3037
*
* property pos:
* def __get__(self): return self.pos # <<<<<<<<<<<<<<
* property pileups:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3037);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3041
+/* "csamtools.pyx":3041
* property pileups:
* '''list of reads (:class:`pysam.PileupRead`) aligned to this column'''
* def __get__(self): # <<<<<<<<<<<<<<
* pileups = []
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self) {
int __pyx_v_x;
PyObject *__pyx_v_pileups = NULL;
PyObject *__pyx_r = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3041);
- /* "pysam/csamtools.pyx":3043
+ /* "csamtools.pyx":3043
* def __get__(self):
* cdef int x
* pileups = [] # <<<<<<<<<<<<<<
* if self.plp[0] == NULL:
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_pileups = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3045
+ /* "csamtools.pyx":3045
* pileups = []
*
* if self.plp[0] == NULL: # <<<<<<<<<<<<<<
* raise ValueError("PileupProxy accessed after iterator finished")
*
*/
- __pyx_t_2 = ((__pyx_v_self->plp[0]) == NULL);
+ __pyx_t_2 = ((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0]) == NULL);
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":3046
+ /* "csamtools.pyx":3046
*
* if self.plp[0] == NULL:
* raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<<
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
- /* "pysam/csamtools.pyx":3050
+ /* "csamtools.pyx":3050
* # warning: there could be problems if self.n and self.buf are
* # out of sync.
* for x from 0 <= x < self.n_pu: # <<<<<<<<<<<<<<
* pileups.append( makePileupRead( &(self.plp[0][x])) )
* return pileups
*/
- __pyx_t_3 = __pyx_v_self->n_pu;
+ __pyx_t_3 = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":3051
+ /* "csamtools.pyx":3051
* # out of sync.
* for x from 0 <= x < self.n_pu:
* pileups.append( makePileupRead( &(self.plp[0][x])) ) # <<<<<<<<<<<<<<
* return pileups
*
*/
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_makePileupRead((&((__pyx_v_self->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_pileups) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "pysam/csamtools.pyx":3052
+ /* "csamtools.pyx":3052
* for x from 0 <= x < self.n_pu:
* pileups.append( makePileupRead( &(self.plp[0][x])) )
* return pileups # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupProxy.pileups.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupProxy.pileups.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_pileups);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead___init__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3058
+/* "csamtools.pyx":3058
* '''
*
* def __init__(self): # <<<<<<<<<<<<<<
*
*/
-static int __pyx_pf_5pysam_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 3058);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- /* "pysam/csamtools.pyx":3059
+ /* "csamtools.pyx":3059
*
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3061
+/* "csamtools.pyx":3061
* raise TypeError("This class cannot be instantiated from Python")
*
* def __str__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 3061);
- /* "pysam/csamtools.pyx":3062
+ /* "csamtools.pyx":3062
*
* def __str__(self):
* return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) ) # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
__pyx_t_7 = 0;
__pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3066
+/* "csamtools.pyx":3066
* property alignment:
* """a :class:`pysam.AlignedRead` object of the aligned read"""
* def __get__(self): # <<<<<<<<<<<<<<
* property qpos:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3066);
- /* "pysam/csamtools.pyx":3067
+ /* "csamtools.pyx":3067
* """a :class:`pysam.AlignedRead` object of the aligned read"""
* def __get__(self):
* return self._alignment # <<<<<<<<<<<<<<
* """position of the read base at the pileup site, 0-based"""
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->_alignment));
- __pyx_r = ((PyObject *)__pyx_v_self->_alignment);
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment));
+ __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3070
+/* "csamtools.pyx":3070
* property qpos:
* """position of the read base at the pileup site, 0-based"""
* def __get__(self): # <<<<<<<<<<<<<<
* property indel:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3070);
- /* "pysam/csamtools.pyx":3071
+ /* "csamtools.pyx":3071
* """position of the read base at the pileup site, 0-based"""
* def __get__(self):
* return self._qpos # <<<<<<<<<<<<<<
* """indel length; 0 for no indel, positive for ins and negative for del"""
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.qpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.qpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3074
+/* "csamtools.pyx":3074
* property indel:
* """indel length; 0 for no indel, positive for ins and negative for del"""
* def __get__(self): # <<<<<<<<<<<<<<
* property is_del:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3074);
- /* "pysam/csamtools.pyx":3075
+ /* "csamtools.pyx":3075
* """indel length; 0 for no indel, positive for ins and negative for del"""
* def __get__(self):
* return self._indel # <<<<<<<<<<<<<<
* """1 iff the base on the padded read is a deletion"""
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3075; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3075; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.indel.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.indel.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3078
+/* "csamtools.pyx":3078
* property is_del:
* """1 iff the base on the padded read is a deletion"""
* def __get__(self): # <<<<<<<<<<<<<<
* property is_head:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3078);
- /* "pysam/csamtools.pyx":3079
+ /* "csamtools.pyx":3079
* """1 iff the base on the padded read is a deletion"""
* def __get__(self):
* return self._is_del # <<<<<<<<<<<<<<
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.is_del.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.is_del.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3081
+/* "csamtools.pyx":3081
* return self._is_del
* property is_head:
* def __get__(self): # <<<<<<<<<<<<<<
* property is_tail:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3081);
- /* "pysam/csamtools.pyx":3082
+ /* "csamtools.pyx":3082
* property is_head:
* def __get__(self):
* return self._is_head # <<<<<<<<<<<<<<
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.is_head.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.is_head.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3084
+/* "csamtools.pyx":3084
* return self._is_head
* property is_tail:
* def __get__(self): # <<<<<<<<<<<<<<
* property level:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3084);
- /* "pysam/csamtools.pyx":3085
+ /* "csamtools.pyx":3085
* property is_tail:
* def __get__(self):
* return self._is_tail # <<<<<<<<<<<<<<
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.is_tail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.is_tail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3087
+/* "csamtools.pyx":3087
* return self._is_tail
* property level:
* def __get__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3087);
- /* "pysam/csamtools.pyx":3088
+ /* "csamtools.pyx":3088
* property level:
* def __get__(self):
* return self._level # <<<<<<<<<<<<<<
* class Outs:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.PileupRead.level.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.PileupRead.level.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs___init__)};
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3092
+ * class Outs:
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1): # <<<<<<<<<<<<<<
+ * self.streams = []
+ * self.id = id
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_4Outs___init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs___init__)};
+static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_id = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__");
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3092);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
PyObject* values[2] = {0,0};
- values[1] = ((PyObject *)((PyObject *)__pyx_int_1));
+ values[1] = ((PyObject *)__pyx_int_1);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs___init__(__pyx_self, __pyx_v_self, __pyx_v_id);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3092
- * class Outs:
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1): # <<<<<<<<<<<<<<
- * self.streams = []
- * self.id = id
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
- __Pyx_TraceCall("__init__", __pyx_f[0], 3092);
- /* "pysam/csamtools.pyx":3093
+ /* "csamtools.pyx":3093
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
* self.streams = [] # <<<<<<<<<<<<<<
*
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__streams, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3094
+ /* "csamtools.pyx":3094
* def __init__(self, id = 1):
* self.streams = []
* self.id = id # <<<<<<<<<<<<<<
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_4Outs_2setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_3setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_3setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_2setdevice)};
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3096
+ * self.id = id
+ *
+ * def setdevice(self, filename): # <<<<<<<<<<<<<<
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_1setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_1setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pf_9csamtools_4Outs_1setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_1setdevice)};
+static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setdevice (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setdevice");
+ __Pyx_TraceCall("setdevice", __pyx_f[0], 3096);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_2setdevice(__pyx_self, __pyx_v_self, __pyx_v_filename);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3096
- * self.id = id
- *
- * def setdevice(self, filename): # <<<<<<<<<<<<<<
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
- */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
- PyObject *__pyx_v_fd = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setdevice", 0);
- __Pyx_TraceCall("setdevice", __pyx_f[0], 3096);
-
- /* "pysam/csamtools.pyx":3098
+ /* "csamtools.pyx":3098
* def setdevice(self, filename):
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
__pyx_v_fd = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3099
+ /* "csamtools.pyx":3099
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY)
* self.setfd(fd) # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_fd);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_4Outs_4setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_5setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_5setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_4setfile)};
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3101
+ * self.setfd(fd)
+ *
+ * def setfile(self, filename): # <<<<<<<<<<<<<<
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_2setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_2setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pf_9csamtools_4Outs_2setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_2setfile)};
+static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setfile (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfile");
+ __Pyx_TraceCall("setfile", __pyx_f[0], 3101);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_4setfile(__pyx_self, __pyx_v_self, __pyx_v_filename);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3101
- * self.setfd(fd)
- *
- * def setfile(self, filename): # <<<<<<<<<<<<<<
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
- */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
- PyObject *__pyx_v_fd = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfile", 0);
- __Pyx_TraceCall("setfile", __pyx_f[0], 3101);
-
- /* "pysam/csamtools.pyx":3103
+ /* "csamtools.pyx":3103
* def setfile(self, filename):
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660); # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
__pyx_v_fd = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3104
+ /* "csamtools.pyx":3104
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
* self.setfd(fd) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_fd);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_4Outs_6setfd[] = "Outs.setfd(self, fd)";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_7setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_7setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_6setfd)};
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3106
+ * self.setfd(fd)
+ *
+ * def setfd(self, fd): # <<<<<<<<<<<<<<
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_3setfd[] = "Outs.setfd(self, fd)";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_3setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pf_9csamtools_4Outs_3setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_3setfd)};
+static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_fd = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_ofd = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setfd (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfd");
+ __Pyx_TraceCall("setfd", __pyx_f[0], 3106);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fd)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fd);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_6setfd(__pyx_self, __pyx_v_self, __pyx_v_fd);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3106
- * self.setfd(fd)
- *
- * def setfd(self, fd): # <<<<<<<<<<<<<<
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd) {
- PyObject *__pyx_v_ofd = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfd", 0);
- __Pyx_TraceCall("setfd", __pyx_f[0], 3106);
- /* "pysam/csamtools.pyx":3107
+ /* "csamtools.pyx":3107
*
* def setfd(self, fd):
* ofd = os.dup(self.id) # Save old stream on new unit. # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__pyx_v_ofd = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3108
+ /* "csamtools.pyx":3108
* def setfd(self, fd):
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd) # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3109
+ /* "csamtools.pyx":3109
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd)
* sys.stdout.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3110
+ /* "csamtools.pyx":3110
* self.streams.append(ofd)
* sys.stdout.flush() # Buffered data goes to old stream.
* sys.stderr.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3111
+ /* "csamtools.pyx":3111
* sys.stdout.flush() # Buffered data goes to old stream.
* sys.stderr.flush() # Buffered data goes to old stream.
* os.dup2(fd, self.id) # Open unit 1 on new stream. # <<<<<<<<<<<<<<
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3112
+ /* "csamtools.pyx":3112
* sys.stderr.flush() # Buffered data goes to old stream.
* os.dup2(fd, self.id) # Open unit 1 on new stream.
* os.close(fd) # Close other unit (look out, caller.) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_ofd);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_4Outs_8restore[] = "Outs.restore(self)\nrestore previous output stream";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_9restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_9restore, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_8restore)};
-static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("restore (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_8restore(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3114
+/* "csamtools.pyx":3114
* os.close(fd) # Close other unit (look out, caller.)
*
* def restore(self): # <<<<<<<<<<<<<<
* if self.streams:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_4restore[] = "Outs.restore(self)\nrestore previous output stream";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_4restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pf_9csamtools_4Outs_4restore, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_4restore)};
+static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("restore", 0);
+ __Pyx_RefNannySetupContext("restore");
__Pyx_TraceCall("restore", __pyx_f[0], 3114);
+ __pyx_self = __pyx_self;
- /* "pysam/csamtools.pyx":3116
+ /* "csamtools.pyx":3116
* def restore(self):
* '''restore previous output stream'''
* if self.streams: # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":3119
+ /* "csamtools.pyx":3119
* # the following was not sufficient, hence flush both stderr and stdout
* # os.fsync( self.id )
* sys.stdout.flush() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3120
+ /* "csamtools.pyx":3120
* # os.fsync( self.id )
* sys.stdout.flush()
* sys.stderr.flush() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3121
+ /* "csamtools.pyx":3121
* sys.stdout.flush()
* sys.stderr.flush()
* os.dup2(self.streams[-1], self.id) # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3122
+ /* "csamtools.pyx":3122
* sys.stderr.flush()
* os.dup2(self.streams[-1], self.id)
* os.close(self.streams[-1]) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3123
+ /* "csamtools.pyx":3123
* os.dup2(self.streams[-1], self.id)
* os.close(self.streams[-1])
* del self.streams[-1] # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_DelItemInt(__pyx_t_3, -1, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("pysam.csamtools.Outs.restore", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.Outs.restore", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5pysam_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout to capture it \n from samtools. If for some reason stdout disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n\n .. note::\n This method captures stdout and stderr using temporary files,\n which are then read into memory in their entirety. This method\n is slow and might cause large memory overhead.\n\n See http://bytes.com/topic/c/answers/487231-how-capture-stdout-temporarily\n on the topic of redirecting stderr/stdout.\n ";
-static PyMethodDef __pyx_mdef_5pysam_9csamtools_1_samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_1_samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools__samtools_dispatch)};
-static PyObject *__pyx_pw_5pysam_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3125
+ * del self.streams[-1]
+ *
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
+ * args = (),
+ * catch_stdout = True ):
+ */
+
+static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout to capture it \n from samtools. If for some reason stdout disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n\n .. note::\n This method captures stdout and stderr using temporary files,\n which are then read into memory in their entirety. This method\n is slow and might cause large memory overhead.\n\n See http://bytes.com/topic/c/answers/487231-how-capture-stdout-temporarily\n on the topic of redirecting stderr/stdout.\n ";
+static PyMethodDef __pyx_mdef_9csamtools__samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pf_9csamtools__samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools__samtools_dispatch)};
+static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_method = 0;
PyObject *__pyx_v_args = 0;
PyObject *__pyx_v_catch_stdout = 0;
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_stderr_h = NULL;
+ PyObject *__pyx_v_stderr_f = NULL;
+ PyObject *__pyx_v_stdout_h = NULL;
+ PyObject *__pyx_v_stdout_f = NULL;
+ PyObject *__pyx_v_stdout_save = NULL;
+ char **__pyx_v_cargs;
+ int __pyx_v_i;
+ int __pyx_v_n;
+ int __pyx_v_retval;
+ PyObject *__pyx_v_inf = NULL;
+ PyObject *__pyx_v_out_stdout = NULL;
+ PyObject *__pyx_v_out_stderr = NULL;
+ PyObject *__pyx_v_a = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_samtools_dispatch (wrapper)", 0);
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *(*__pyx_t_7)(PyObject *);
+ int __pyx_t_8;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ PyObject *(*__pyx_t_13)(PyObject *);
+ char *__pyx_t_14;
+ PyObject *__pyx_t_15 = NULL;
+ PyObject *__pyx_t_16 = NULL;
+ PyObject *__pyx_t_17 = NULL;
+ PyObject *__pyx_t_18 = NULL;
+ PyObject *__pyx_t_19 = NULL;
+ PyObject *__pyx_t_20 = NULL;
+ PyObject *__pyx_t_21 = NULL;
+ PyObject *__pyx_t_22 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_samtools_dispatch");
+ __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
PyObject* values[3] = {0,0,0};
- /* "pysam/csamtools.pyx":3126
+ /* "csamtools.pyx":3126
*
* def _samtools_dispatch( method,
* args = (), # <<<<<<<<<<<<<<
values[2] = __pyx_k_176;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_5pysam_9csamtools__samtools_dispatch(__pyx_self, __pyx_v_method, __pyx_v_args, __pyx_v_catch_stdout);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3125
- * del self.streams[-1]
- *
- * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
- * args = (),
- * catch_stdout = True ):
- */
-
-static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout) {
- PyObject *__pyx_v_stderr_h = NULL;
- PyObject *__pyx_v_stderr_f = NULL;
- PyObject *__pyx_v_stdout_h = NULL;
- PyObject *__pyx_v_stdout_f = NULL;
- PyObject *__pyx_v_stdout_save = NULL;
- char **__pyx_v_cargs;
- int __pyx_v_i;
- int __pyx_v_n;
- int __pyx_v_retval;
- PyObject *__pyx_v_inf = NULL;
- PyObject *__pyx_v_out_stdout = NULL;
- PyObject *__pyx_v_out_stderr = NULL;
- PyObject *__pyx_v_a = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *(*__pyx_t_7)(PyObject *);
- int __pyx_t_8;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- Py_ssize_t __pyx_t_12;
- PyObject *(*__pyx_t_13)(PyObject *);
- char *__pyx_t_14;
- PyObject *__pyx_t_15 = NULL;
- PyObject *__pyx_t_16 = NULL;
- PyObject *__pyx_t_17 = NULL;
- PyObject *__pyx_t_18 = NULL;
- PyObject *__pyx_t_19 = NULL;
- PyObject *__pyx_t_20 = NULL;
- PyObject *__pyx_t_21 = NULL;
- PyObject *__pyx_t_22 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_samtools_dispatch", 0);
- __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125);
__Pyx_INCREF(__pyx_v_method);
__Pyx_INCREF(__pyx_v_args);
__Pyx_INCREF(__pyx_v_catch_stdout);
- /* "pysam/csamtools.pyx":3151
+ /* "csamtools.pyx":3151
*
* # some special cases
* if method == "index": # <<<<<<<<<<<<<<
* if not os.path.exists( args[0] ):
* raise IOError( "No such file or directory: '%s'" % args[0] )
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_method, ((PyObject *)__pyx_n_s__index), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_method, ((PyObject *)__pyx_n_s__index), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":3152
+ /* "csamtools.pyx":3152
* # some special cases
* if method == "index":
* if not os.path.exists( args[0] ): # <<<<<<<<<<<<<<
* raise IOError( "No such file or directory: '%s'" % args[0] )
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __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_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = (!__pyx_t_2);
+ __pyx_t_5 = (!__pyx_t_1);
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":3153
+ /* "csamtools.pyx":3153
* if method == "index":
* if not os.path.exists( args[0] ):
* raise IOError( "No such file or directory: '%s'" % args[0] ) # <<<<<<<<<<<<<<
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
- goto __pyx_L3;
+ __pyx_L7:;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":3156
+ /* "csamtools.pyx":3156
*
* # redirect stderr and stdout to file
* stderr_h, stderr_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_1 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_3);
- __Pyx_INCREF(__pyx_t_1);
- #else
- __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
+ index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
- index = 1; __pyx_t_1 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L6_unpacking_done;
- __pyx_L5_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L6_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__pyx_v_stderr_h = __pyx_t_3;
__pyx_t_3 = 0;
- __pyx_v_stderr_f = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_stderr_f = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":3157
+ /* "csamtools.pyx":3157
* # redirect stderr and stdout to file
* stderr_h, stderr_f = tempfile.mkstemp()
* pysam_set_stderr( stderr_h ) # <<<<<<<<<<<<<<
__pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_v_stderr_h); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
pysam_set_stderr(__pyx_t_8);
- /* "pysam/csamtools.pyx":3159
+ /* "csamtools.pyx":3159
* pysam_set_stderr( stderr_h )
*
* if catch_stdout: # <<<<<<<<<<<<<<
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":3160
+ /* "csamtools.pyx":3160
*
* if catch_stdout:
* stdout_h, stdout_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
*/
__pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
} else {
- __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
__pyx_t_3 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_3);
- #else
- __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_1)) goto __pyx_L8_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
+ index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L11_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_2);
+ index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L11_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
+ goto __pyx_L12_unpacking_done;
+ __pyx_L11_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ __pyx_L12_unpacking_done:;
}
- __pyx_v_stdout_h = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_stdout_h = __pyx_t_2;
+ __pyx_t_2 = 0;
__pyx_v_stdout_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3161
+ /* "csamtools.pyx":3161
* if catch_stdout:
* stdout_h, stdout_f = tempfile.mkstemp()
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
- /* "pysam/csamtools.pyx":3162
+ /* "csamtools.pyx":3162
* stdout_h, stdout_f = tempfile.mkstemp()
* try:
* stdout_save = Outs( sys.stdout.fileno() ) # <<<<<<<<<<<<<<
* stdout_save.setfd( stdout_h )
* except AttributeError:
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_v_stdout_save = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_stdout_save = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":3163
+ /* "csamtools.pyx":3163
* try:
* stdout_save = Outs( sys.stdout.fileno() )
* stdout_save.setfd( stdout_h ) # <<<<<<<<<<<<<<
* except AttributeError:
* # stdout has already been redirected
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(__pyx_v_stdout_h);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_h);
__Pyx_GIVEREF(__pyx_v_stdout_h);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L17_try_end;
- __pyx_L10_error:;
+ goto __pyx_L20_try_end;
+ __pyx_L13_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3164
+ /* "csamtools.pyx":3164
* stdout_save = Outs( sys.stdout.fileno() )
* stdout_save.setfd( stdout_h )
* except AttributeError: # <<<<<<<<<<<<<<
*/
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_AttributeError);
if (__pyx_t_8) {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_2);
- /* "pysam/csamtools.pyx":3166
+ /* "csamtools.pyx":3166
* except AttributeError:
* # stdout has already been redirected
* catch_stdout = False # <<<<<<<<<<<<<<
*
* # patch for `samtools view`
*/
- __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3166; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3166; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_v_catch_stdout);
__pyx_v_catch_stdout = __pyx_t_6;
__pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L11_exception_handled;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L14_exception_handled;
}
- __pyx_L12_except_error:;
+ __pyx_L15_except_error:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
goto __pyx_L1_error;
- __pyx_L11_exception_handled:;
+ __pyx_L14_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
- __pyx_L17_try_end:;
+ __pyx_L20_try_end:;
}
- /* "pysam/csamtools.pyx":3171
+ /* "csamtools.pyx":3171
* # samtools `view` closes stdout, from which I can not
* # recover. Thus redirect output to file with -o option.
* if method == "view": # <<<<<<<<<<<<<<
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
* args = ( "-o", stdout_f ) + args
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_method, ((PyObject *)__pyx_n_s__view), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_method, ((PyObject *)__pyx_n_s__view), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":3172
+ /* "csamtools.pyx":3172
* # recover. Thus redirect output to file with -o option.
* if method == "view":
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
* args = ( "-o", stdout_f ) + args
*
*/
- __pyx_t_5 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_kp_s_178), __pyx_v_args, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_args, ((PyObject *)__pyx_kp_s_178)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_180), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_Raise(__pyx_t_1, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_180), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L21;
+ goto __pyx_L24;
}
- __pyx_L21:;
+ __pyx_L24:;
- /* "pysam/csamtools.pyx":3173
+ /* "csamtools.pyx":3173
* if method == "view":
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
* args = ( "-o", stdout_f ) + args # <<<<<<<<<<<<<<
*
* # do the function call to samtools
*/
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_178));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_178));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_178));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_178));
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_1), __pyx_v_args); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_2), __pyx_v_args); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_args);
__pyx_v_args = __pyx_t_3;
__pyx_t_3 = 0;
- goto __pyx_L20;
+ goto __pyx_L23;
}
- __pyx_L20:;
- goto __pyx_L7;
+ __pyx_L23:;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
- /* "pysam/csamtools.pyx":3179
+ /* "csamtools.pyx":3179
* cdef int i, n, retval
*
* n = len(args) # <<<<<<<<<<<<<<
__pyx_t_12 = PyObject_Length(__pyx_v_args); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_n = __pyx_t_12;
- /* "pysam/csamtools.pyx":3180
+ /* "csamtools.pyx":3180
*
* n = len(args)
* method = _force_cmdline_bytes(method) # <<<<<<<<<<<<<<
* args = [ _force_cmdline_bytes(a) for a in args ]
*
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_cmdline_bytes(__pyx_v_method)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)__pyx_f_9csamtools__force_cmdline_bytes(__pyx_v_method)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_v_method);
__pyx_v_method = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3181
+ /* "csamtools.pyx":3181
* n = len(args)
* method = _force_cmdline_bytes(method)
* args = [ _force_cmdline_bytes(a) for a in args ] # <<<<<<<<<<<<<<
* # allocate two more for first (dummy) argument (contains command)
*/
__pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
if (PyList_CheckExact(__pyx_v_args) || PyTuple_CheckExact(__pyx_v_args)) {
- __pyx_t_1 = __pyx_v_args; __Pyx_INCREF(__pyx_t_1); __pyx_t_12 = 0;
+ __pyx_t_2 = __pyx_v_args; __Pyx_INCREF(__pyx_t_2); __pyx_t_12 = 0;
__pyx_t_13 = NULL;
} else {
- __pyx_t_12 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ __pyx_t_12 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_13 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_13 && PyList_CheckExact(__pyx_t_1)) {
- if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_13 && PyTuple_CheckExact(__pyx_t_1)) {
- if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
} else {
- __pyx_t_4 = __pyx_t_13(__pyx_t_1);
+ __pyx_t_4 = __pyx_t_13(__pyx_t_2);
if (unlikely(!__pyx_t_4)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
__Pyx_XDECREF(__pyx_v_a);
__pyx_v_a = __pyx_t_4;
__pyx_t_4 = 0;
- __pyx_t_4 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_cmdline_bytes(__pyx_v_a)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((PyObject *)__pyx_f_9csamtools__force_cmdline_bytes(__pyx_v_a)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = ((PyObject *)__pyx_t_3);
- __Pyx_INCREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_3));
__Pyx_DECREF(__pyx_v_args);
- __pyx_v_args = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_args = ((PyObject *)__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3184
+ /* "csamtools.pyx":3184
*
* # allocate two more for first (dummy) argument (contains command)
* cargs = <char**>calloc( n+2, sizeof( char *) ) # <<<<<<<<<<<<<<
*/
__pyx_v_cargs = ((char **)calloc((__pyx_v_n + 2), (sizeof(char *))));
- /* "pysam/csamtools.pyx":3185
+ /* "csamtools.pyx":3185
* # allocate two more for first (dummy) argument (contains command)
* cargs = <char**>calloc( n+2, sizeof( char *) )
* cargs[0] = "samtools" # <<<<<<<<<<<<<<
*/
(__pyx_v_cargs[0]) = __pyx_k__samtools;
- /* "pysam/csamtools.pyx":3186
+ /* "csamtools.pyx":3186
* cargs = <char**>calloc( n+2, sizeof( char *) )
* cargs[0] = "samtools"
* cargs[1] = method # <<<<<<<<<<<<<<
__pyx_t_14 = PyBytes_AsString(__pyx_v_method); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
(__pyx_v_cargs[1]) = __pyx_t_14;
- /* "pysam/csamtools.pyx":3187
+ /* "csamtools.pyx":3187
* cargs[0] = "samtools"
* cargs[1] = method
* for i from 0 <= i < n: cargs[i+2] = args[i] # <<<<<<<<<<<<<<
*/
__pyx_t_8 = __pyx_v_n;
for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_8; __pyx_v_i++) {
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_14 = PyBytes_AsString(__pyx_t_1); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_14 = PyBytes_AsString(__pyx_t_3); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
(__pyx_v_cargs[(__pyx_v_i + 2)]) = __pyx_t_14;
}
- /* "pysam/csamtools.pyx":3189
+ /* "csamtools.pyx":3189
* for i from 0 <= i < n: cargs[i+2] = args[i]
*
* retval = pysam_dispatch(n+2, cargs) # <<<<<<<<<<<<<<
*/
__pyx_v_retval = pysam_dispatch((__pyx_v_n + 2), __pyx_v_cargs);
- /* "pysam/csamtools.pyx":3190
+ /* "csamtools.pyx":3190
*
* retval = pysam_dispatch(n+2, cargs)
* free( cargs ) # <<<<<<<<<<<<<<
*/
free(__pyx_v_cargs);
- /* "pysam/csamtools.pyx":3194
+ /* "csamtools.pyx":3194
* # restore stdout/stderr. This will also flush, so
* # needs to be before reading back the file contents
* if catch_stdout: # <<<<<<<<<<<<<<
*/
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
+ if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":3195
+ /* "csamtools.pyx":3195
* # needs to be before reading back the file contents
* if catch_stdout:
* stdout_save.restore() # <<<<<<<<<<<<<<
* try:
* with open( stdout_f, "r") as inf:
*/
- if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":3196
+ /* "csamtools.pyx":3196
* if catch_stdout:
* stdout_save.restore()
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_9);
/*try:*/ {
- /* "pysam/csamtools.pyx":3197
+ /* "csamtools.pyx":3197
* stdout_save.restore()
* try:
* with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
*/
/*with:*/ {
- if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;} }
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;} }__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____enter__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L38_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L38_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_18);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_4);
- __pyx_v_inf = __pyx_t_4;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_inf = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3198
+ /* "csamtools.pyx":3198
* try:
* with open( stdout_f, "r") as inf:
* out_stdout = inf.readlines() # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf:
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_v_out_stdout = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L44_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L44_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_v_out_stdout = __pyx_t_2;
+ __pyx_t_2 = 0;
}
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- goto __pyx_L48_try_end;
- __pyx_L41_error:;
+ goto __pyx_L51_try_end;
+ __pyx_L44_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":3197
+ /* "csamtools.pyx":3197
* stdout_save.restore()
* try:
* with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
*/
/*except:*/ {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_3, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_INCREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_INCREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
__pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
__Pyx_GOTREF(__pyx_t_19);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
- __pyx_t_2 = (!__pyx_t_5);
- if (__pyx_t_2) {
- __Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_4);
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ __pyx_t_1 = (!__pyx_t_5);
+ if (__pyx_t_1) {
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_3);
- __Pyx_ErrRestore(__pyx_t_1, __pyx_t_4, __pyx_t_3);
- __pyx_t_1 = 0; __pyx_t_4 = 0; __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
- goto __pyx_L52;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_ErrRestore(__pyx_t_2, __pyx_t_3, __pyx_t_4);
+ __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ goto __pyx_L54;
}
- __pyx_L52:;
+ __pyx_L54:;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L42_exception_handled;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ goto __pyx_L45_exception_handled;
}
- __pyx_L43_except_error:;
+ __pyx_L46_except_error:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- goto __pyx_L27_error;
- __pyx_L42_exception_handled:;
+ goto __pyx_L30_error;
+ __pyx_L45_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- __pyx_L48_try_end:;
+ __pyx_L51_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
__pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_181, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
__Pyx_GOTREF(__pyx_t_18);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_18);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
}
}
- goto __pyx_L53;
- __pyx_L35_error:;
+ goto __pyx_L55;
+ __pyx_L38_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L27_error;
- __pyx_L53:;
+ goto __pyx_L30_error;
+ __pyx_L55:;
}
}
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L34_try_end;
- __pyx_L27_error:;
+ goto __pyx_L37_try_end;
+ __pyx_L30_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3199
+ /* "csamtools.pyx":3199
* with open( stdout_f, "r") as inf:
* out_stdout = inf.readlines()
* except UnicodeDecodeError: # <<<<<<<<<<<<<<
*/
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
if (__pyx_t_8) {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_2);
- /* "pysam/csamtools.pyx":3200
+ /* "csamtools.pyx":3200
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
* out_stdout = inf.read()
*/
/*with:*/ {
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_stdout_f);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L58_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_21 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L58_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_21);
__Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_21;
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __pyx_v_inf = __pyx_t_20;
+ __pyx_t_20 = 0;
- /* "pysam/csamtools.pyx":3202
+ /* "csamtools.pyx":3202
* with open( stdout_f, "rb") as inf:
* # read binary output
* out_stdout = inf.read() # <<<<<<<<<<<<<<
* os.remove( stdout_f )
* else:
*/
- __pyx_t_21 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
+ __pyx_t_20 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L64_error;}
__Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L64_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_v_out_stdout);
- __pyx_v_out_stdout = __pyx_t_20;
- __pyx_t_20 = 0;
+ __pyx_v_out_stdout = __pyx_t_6;
+ __pyx_t_6 = 0;
}
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
- goto __pyx_L69_try_end;
- __pyx_L62_error:;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ goto __pyx_L71_try_end;
+ __pyx_L64_error:;
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":3200
+ /* "csamtools.pyx":3200
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
* out_stdout = inf.read()
*/
/*except:*/ {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_20, &__pyx_t_21, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_20, &__pyx_t_21) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_20);
__Pyx_GOTREF(__pyx_t_21);
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_22));
+ __Pyx_INCREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_20);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_20);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_20);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_INCREF(__pyx_t_21);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_21);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_21);
__Pyx_GIVEREF(__pyx_t_21);
- __Pyx_INCREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
__pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
__Pyx_GOTREF(__pyx_t_19);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
- __pyx_t_5 = (!__pyx_t_2);
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ __pyx_t_5 = (!__pyx_t_1);
if (__pyx_t_5) {
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_GIVEREF(__pyx_t_21);
- __Pyx_GIVEREF(__pyx_t_6);
- __Pyx_ErrRestore(__pyx_t_20, __pyx_t_21, __pyx_t_6);
- __pyx_t_20 = 0; __pyx_t_21 = 0; __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
- goto __pyx_L73;
+ __Pyx_ErrRestore(__pyx_t_6, __pyx_t_20, __pyx_t_21);
+ __pyx_t_6 = 0; __pyx_t_20 = 0; __pyx_t_21 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ goto __pyx_L74;
}
- __pyx_L73:;
+ __pyx_L74:;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L63_exception_handled;
+ goto __pyx_L65_exception_handled;
}
- __pyx_L64_except_error:;
+ __pyx_L66_except_error:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- goto __pyx_L29_except_error;
- __pyx_L63_exception_handled:;
+ goto __pyx_L32_except_error;
+ __pyx_L65_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- __pyx_L69_try_end:;
+ __pyx_L71_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
__pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_182, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
}
}
- goto __pyx_L74;
- __pyx_L56_error:;
+ goto __pyx_L75;
+ __pyx_L58_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L29_except_error;
- __pyx_L74:;
+ goto __pyx_L32_except_error;
+ __pyx_L75:;
}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L28_exception_handled;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L31_exception_handled;
}
- __pyx_L29_except_error:;
+ __pyx_L32_except_error:;
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
goto __pyx_L1_error;
- __pyx_L28_exception_handled:;
+ __pyx_L31_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
- __pyx_L34_try_end:;
+ __pyx_L37_try_end:;
}
- /* "pysam/csamtools.pyx":3203
+ /* "csamtools.pyx":3203
* # read binary output
* out_stdout = inf.read()
* os.remove( stdout_f ) # <<<<<<<<<<<<<<
* else:
* out_stdout = []
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__remove); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L26;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ goto __pyx_L29;
}
/*else*/ {
- /* "pysam/csamtools.pyx":3205
+ /* "csamtools.pyx":3205
* os.remove( stdout_f )
* else:
* out_stdout = [] # <<<<<<<<<<<<<<
*
* # get error messages
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_out_stdout = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_v_out_stdout = ((PyObject *)__pyx_t_4);
+ __pyx_t_4 = 0;
}
- __pyx_L26:;
+ __pyx_L29:;
- /* "pysam/csamtools.pyx":3208
+ /* "csamtools.pyx":3208
*
* # get error messages
* pysam_unset_stderr() # <<<<<<<<<<<<<<
*/
pysam_unset_stderr();
- /* "pysam/csamtools.pyx":3209
+ /* "csamtools.pyx":3209
* # get error messages
* pysam_unset_stderr()
* try: # <<<<<<<<<<<<<<
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
- /* "pysam/csamtools.pyx":3210
+ /* "csamtools.pyx":3210
* pysam_unset_stderr()
* try:
* with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
*/
/*with:*/ {
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_stderr_f);
__Pyx_GIVEREF(__pyx_v_stderr_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_1 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____enter__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L83_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L83_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____enter__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L84_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L84_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_18);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_4;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_inf = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":3211
+ /* "csamtools.pyx":3211
* try:
* with open( stderr_f, "r") as inf:
* out_stderr = inf.readlines() # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf:
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L89_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L90_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L90_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L89_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_v_out_stderr = __pyx_t_1;
- __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_out_stderr = __pyx_t_4;
+ __pyx_t_4 = 0;
}
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- goto __pyx_L96_try_end;
- __pyx_L89_error:;
+ goto __pyx_L97_try_end;
+ __pyx_L90_error:;
__Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3210
+ /* "csamtools.pyx":3210
* pysam_unset_stderr()
* try:
* with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
*/
/*except:*/ {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_2, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
__Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_21 = PyTuple_New(3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_21));
__Pyx_INCREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_INCREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_21, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_21, 2, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_21, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
__Pyx_GOTREF(__pyx_t_19);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
- __pyx_t_2 = (!__pyx_t_5);
- if (__pyx_t_2) {
- __Pyx_GIVEREF(__pyx_t_1);
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
+ __pyx_t_1 = (!__pyx_t_5);
+ if (__pyx_t_1) {
__Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_3);
- __Pyx_ErrRestore(__pyx_t_1, __pyx_t_4, __pyx_t_3);
- __pyx_t_1 = 0; __pyx_t_4 = 0; __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ __Pyx_ErrRestore(__pyx_t_4, __pyx_t_2, __pyx_t_3);
+ __pyx_t_4 = 0; __pyx_t_2 = 0; __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
goto __pyx_L100;
}
__pyx_L100:;
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L90_exception_handled;
+ goto __pyx_L91_exception_handled;
}
- __pyx_L91_except_error:;
+ __pyx_L92_except_error:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- goto __pyx_L75_error;
- __pyx_L90_exception_handled:;
+ goto __pyx_L76_error;
+ __pyx_L91_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- __pyx_L96_try_end:;
+ __pyx_L97_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
__pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_183, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
__Pyx_GOTREF(__pyx_t_18);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_18);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
}
}
goto __pyx_L101;
- __pyx_L83_error:;
+ __pyx_L84_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L75_error;
+ goto __pyx_L76_error;
__pyx_L101:;
}
}
/*else:*/ {
- /* "pysam/csamtools.pyx":3218
+ /* "csamtools.pyx":3218
* os.remove( stderr_f )
* else:
* out_stderr = [] # <<<<<<<<<<<<<<
*
* return retval, out_stderr, out_stdout
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3218; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3218; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_XDECREF(__pyx_v_out_stderr);
__pyx_v_out_stderr = ((PyObject *)__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L82_try_end;
- __pyx_L75_error:;
+ goto __pyx_L83_try_end;
+ __pyx_L76_error:;
__Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3212
+ /* "csamtools.pyx":3212
* with open( stderr_f, "r") as inf:
* out_stderr = inf.readlines()
* except UnicodeDecodeError: # <<<<<<<<<<<<<<
*/
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
if (__pyx_t_8) {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":3213
+ /* "csamtools.pyx":3213
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
* out_stderr = inf.read()
*/
/*with:*/ {
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_21 = PyTuple_New(2); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_21));
__Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_v_stderr_f);
__Pyx_GIVEREF(__pyx_v_stderr_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
+ PyTuple_SET_ITEM(__pyx_t_21, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_21 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_21), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
+ __pyx_t_21 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
__Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
/*try:*/ {
{
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_20);
__Pyx_XDECREF(__pyx_v_inf);
__pyx_v_inf = __pyx_t_20;
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __pyx_t_20 = 0;
- /* "pysam/csamtools.pyx":3215
+ /* "csamtools.pyx":3215
* with open( stderr_f, "rb") as inf:
* # read binary output
* out_stderr = inf.read() # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- /* "pysam/csamtools.pyx":3213
+ /* "csamtools.pyx":3213
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
* out_stderr = inf.read()
*/
/*except:*/ {
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
if (__Pyx_GetException(&__pyx_t_21, &__pyx_t_20, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
__Pyx_GOTREF(__pyx_t_21);
__Pyx_GOTREF(__pyx_t_20);
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_22));
__Pyx_INCREF(__pyx_t_21);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_21);
__Pyx_GIVEREF(__pyx_t_21);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
__Pyx_GOTREF(__pyx_t_19);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __pyx_t_5 = (!__pyx_t_2);
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
+ __pyx_t_5 = (!__pyx_t_1);
if (__pyx_t_5) {
__Pyx_GIVEREF(__pyx_t_21);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_ErrRestore(__pyx_t_21, __pyx_t_20, __pyx_t_6);
__pyx_t_21 = 0; __pyx_t_20 = 0; __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- goto __pyx_L121;
+ goto __pyx_L120;
}
- __pyx_L121:;
+ __pyx_L120:;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- goto __pyx_L77_except_error;
+ goto __pyx_L78_except_error;
__pyx_L111_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
if (__pyx_t_15) {
__pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_184, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
}
}
- goto __pyx_L122;
+ goto __pyx_L121;
__pyx_L104_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L77_except_error;
- __pyx_L122:;
+ goto __pyx_L78_except_error;
+ __pyx_L121:;
}
- /* "pysam/csamtools.pyx":3216
+ /* "csamtools.pyx":3216
* # read binary output
* out_stderr = inf.read()
* os.remove( stderr_f ) # <<<<<<<<<<<<<<
* else:
* out_stderr = []
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_20 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__remove); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_20 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__remove); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_stderr_f);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
__Pyx_GIVEREF(__pyx_v_stderr_f);
- __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_21);
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L76_exception_handled;
+ goto __pyx_L77_exception_handled;
}
- __pyx_L77_except_error:;
+ __pyx_L78_except_error:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
goto __pyx_L1_error;
- __pyx_L76_exception_handled:;
+ __pyx_L77_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
- __pyx_L82_try_end:;
+ __pyx_L83_try_end:;
}
- /* "pysam/csamtools.pyx":3220
+ /* "csamtools.pyx":3220
* out_stderr = []
*
* return retval, out_stderr, out_stdout # <<<<<<<<<<<<<<
* cdef class SNPCall:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_out_stderr);
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_out_stderr);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_out_stderr);
__Pyx_GIVEREF(__pyx_v_out_stderr);
__Pyx_INCREF(__pyx_v_out_stdout);
- PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_out_stdout);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_out_stdout);
__Pyx_GIVEREF(__pyx_v_out_stdout);
- __pyx_t_1 = 0;
- __pyx_r = ((PyObject *)__pyx_t_4);
__pyx_t_4 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_20);
__Pyx_XDECREF(__pyx_t_21);
__Pyx_XDECREF(__pyx_t_22);
- __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_stderr_h);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3235
+/* "csamtools.pyx":3235
* property tid:
* '''the chromosome ID as is defined in the header'''
* def __get__(self): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3235);
- /* "pysam/csamtools.pyx":3236
+ /* "csamtools.pyx":3236
* '''the chromosome ID as is defined in the header'''
* def __get__(self):
* return self._tid # <<<<<<<<<<<<<<
* property pos:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3240
+/* "csamtools.pyx":3240
* property pos:
* '''nucleotide position of SNP.'''
* def __get__(self): return self._pos # <<<<<<<<<<<<<<
* property reference_base:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3240);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3244
+/* "csamtools.pyx":3244
* property reference_base:
* '''reference base at pos. ``N`` if no reference sequence supplied.'''
* def __get__(self): return from_string_and_size( &self._reference_base, 1 ) # <<<<<<<<<<<<<<
* property genotype:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3244);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_from_string_and_size((&__pyx_v_self->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.reference_base.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.reference_base.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3248
+/* "csamtools.pyx":3248
* property genotype:
* '''the genotype called.'''
* def __get__(self): return from_string_and_size( &self._genotype, 1 ) # <<<<<<<<<<<<<<
* property consensus_quality:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3248);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_5pysam_9csamtools_from_string_and_size((&__pyx_v_self->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.genotype.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.genotype.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3252
+/* "csamtools.pyx":3252
* property consensus_quality:
* '''the genotype quality (Phred-scaled).'''
* def __get__(self): return self._consensus_quality # <<<<<<<<<<<<<<
* property snp_quality:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3252);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.consensus_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.consensus_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3256
+/* "csamtools.pyx":3256
* property snp_quality:
* '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
* def __get__(self): return self._snp_quality # <<<<<<<<<<<<<<
* property mapping_quality:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3256);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.snp_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.snp_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3260
+/* "csamtools.pyx":3260
* property mapping_quality:
* '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
* def __get__(self): return self._rms_mapping_quality # <<<<<<<<<<<<<<
* property coverage:
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3260);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.mapping_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.mapping_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3264
+/* "csamtools.pyx":3264
* property coverage:
* '''coverage or read depth - the number of reads involved in the call.'''
* def __get__(self): return self._coverage # <<<<<<<<<<<<<<
* def __str__(self):
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3264);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.coverage.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.coverage.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall___str__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3266
+/* "csamtools.pyx":3266
* def __get__(self): return self._coverage
*
* def __str__(self): # <<<<<<<<<<<<<<
* return "\t".join( map(str, (
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall___str__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 3266);
- /* "pysam/csamtools.pyx":3268
+ /* "csamtools.pyx":3268
* def __str__(self):
*
* return "\t".join( map(str, ( # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/csamtools.pyx":3269
+ /* "csamtools.pyx":3269
*
* return "\t".join( map(str, (
* self.tid, # <<<<<<<<<<<<<<
* self.pos,
* self.reference_base,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- /* "pysam/csamtools.pyx":3270
+ /* "csamtools.pyx":3270
* return "\t".join( map(str, (
* self.tid,
* self.pos, # <<<<<<<<<<<<<<
* self.reference_base,
* self.genotype,
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- /* "pysam/csamtools.pyx":3271
+ /* "csamtools.pyx":3271
* self.tid,
* self.pos,
* self.reference_base, # <<<<<<<<<<<<<<
* self.genotype,
* self.consensus_quality,
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- /* "pysam/csamtools.pyx":3272
+ /* "csamtools.pyx":3272
* self.pos,
* self.reference_base,
* self.genotype, # <<<<<<<<<<<<<<
* self.consensus_quality,
* self.snp_quality,
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- /* "pysam/csamtools.pyx":3273
+ /* "csamtools.pyx":3273
* self.reference_base,
* self.genotype,
* self.consensus_quality, # <<<<<<<<<<<<<<
* self.snp_quality,
* self.mapping_quality,
*/
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "pysam/csamtools.pyx":3274
+ /* "csamtools.pyx":3274
* self.genotype,
* self.consensus_quality,
* self.snp_quality, # <<<<<<<<<<<<<<
* self.mapping_quality,
* self.coverage ) ) )
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/csamtools.pyx":3275
+ /* "csamtools.pyx":3275
* self.consensus_quality,
* self.snp_quality,
* self.mapping_quality, # <<<<<<<<<<<<<<
* self.coverage ) ) )
*
*/
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- /* "pysam/csamtools.pyx":3276
+ /* "csamtools.pyx":3276
* self.snp_quality,
* self.mapping_quality,
* self.coverage ) ) ) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_10 = PyTuple_New(8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_3);
__pyx_t_8 = 0;
__pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("pysam.csamtools.SNPCall.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.SNPCall.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":3786
+ * """
+ *
+ * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ *
+ */
+
+static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_reopen;
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ char *__pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__");
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3786);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
if (values[1]) {
__pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
-
- /* "pysam/csamtools.pyx":3786
- * """
- *
- * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- *
- */
__pyx_v_reopen = ((int)1);
}
}
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("pysam.csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- char *__pyx_t_3;
- samfile_t *__pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
- __Pyx_TraceCall("__init__", __pyx_f[0], 3786);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":3787
+ /* "csamtools.pyx":3787
*
* def __init__(self, Samfile samfile, int reopen = True ):
* self.samfile = samfile # <<<<<<<<<<<<<<
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile = __pyx_v_samfile;
- /* "pysam/csamtools.pyx":3789
+ /* "csamtools.pyx":3789
* self.samfile = samfile
*
* if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L3;
+ goto __pyx_L6;
}
/*else*/ {
- /* "pysam/csamtools.pyx":3790
+ /* "csamtools.pyx":3790
*
* if samfile.isbam: mode = b"rb"
* else: mode = b"r" # <<<<<<<<<<<<<<
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L3:;
+ __pyx_L6:;
- /* "pysam/csamtools.pyx":3794
+ /* "csamtools.pyx":3794
* # reopen the file - note that this makes the iterator
* # slow and causes pileup to slow down significantly.
* if reopen: # <<<<<<<<<<<<<<
*/
if (__pyx_v_reopen) {
- /* "pysam/csamtools.pyx":3795
+ /* "csamtools.pyx":3795
* # slow and causes pileup to slow down significantly.
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
__pyx_v_store = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":3796
+ /* "csamtools.pyx":3796
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* assert self.fp != NULL
*/
__pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
- /* "pysam/csamtools.pyx":3797
+ /* "csamtools.pyx":3797
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3798
+ /* "csamtools.pyx":3798
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":3799
+ /* "csamtools.pyx":3799
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L4;
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L7;
}
/*else*/ {
- /* "pysam/csamtools.pyx":3801
+ /* "csamtools.pyx":3801
* self.owns_samfile = True
* else:
* self.fp = samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- __pyx_t_4 = __pyx_v_samfile->samfile;
- __pyx_v_self->fp = __pyx_t_4;
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
- /* "pysam/csamtools.pyx":3802
+ /* "csamtools.pyx":3802
* else:
* self.fp = samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* assert samfile.isbam, "can only IndexReads on bam files"
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L4:;
+ __pyx_L7:;
- /* "pysam/csamtools.pyx":3804
+ /* "csamtools.pyx":3804
* self.owns_samfile = False
*
* assert samfile.isbam, "can only IndexReads on bam files" # <<<<<<<<<<<<<<
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("pysam.csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_12IndexedReads_2build[] = "IndexedReads.build(self)\nbuild index.";
-static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("build (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_12IndexedReads_2build(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3806
+/* "csamtools.pyx":3806
* assert samfile.isbam, "can only IndexReads on bam files"
*
* def build( self ): # <<<<<<<<<<<<<<
*
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_2build(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_12IndexedReads_1build[] = "IndexedReads.build(self)\nbuild index.";
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
int __pyx_v_ret;
bam1_t *__pyx_v_b;
uint64_t __pyx_v_pos;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("build", 0);
+ __Pyx_RefNannySetupContext("build");
__Pyx_TraceCall("build", __pyx_f[0], 3806);
- /* "pysam/csamtools.pyx":3809
+ /* "csamtools.pyx":3809
* '''build index.'''
*
* self.index = collections.defaultdict( list ) # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyList_Type))));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyList_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyList_Type))));
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_GIVEREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_v_self->index);
- __Pyx_DECREF(__pyx_v_self->index);
- __pyx_v_self->index = __pyx_t_3;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
+ __Pyx_DECREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3813
+ /* "csamtools.pyx":3813
* # this method will start indexing from the current file position
* # if you decide
* cdef int ret = 1 # <<<<<<<<<<<<<<
*/
__pyx_v_ret = 1;
- /* "pysam/csamtools.pyx":3814
+ /* "csamtools.pyx":3814
* # if you decide
* cdef int ret = 1
* cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
*/
__pyx_v_b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "pysam/csamtools.pyx":3818
+ /* "csamtools.pyx":3818
* cdef uint64_t pos
*
* while ret > 0: # <<<<<<<<<<<<<<
__pyx_t_4 = (__pyx_v_ret > 0);
if (!__pyx_t_4) break;
- /* "pysam/csamtools.pyx":3819
+ /* "csamtools.pyx":3819
*
* while ret > 0:
* pos = bam_tell( self.fp.x.bam ) # <<<<<<<<<<<<<<
* ret = samread( self.fp, b)
* if ret > 0:
*/
- __pyx_v_pos = bam_tell(__pyx_v_self->fp->x.bam);
+ __pyx_v_pos = bam_tell(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp->x.bam);
- /* "pysam/csamtools.pyx":3820
+ /* "csamtools.pyx":3820
* while ret > 0:
* pos = bam_tell( self.fp.x.bam )
* ret = samread( self.fp, b) # <<<<<<<<<<<<<<
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b ))
*/
- __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_b);
+ __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp, __pyx_v_b);
- /* "pysam/csamtools.pyx":3821
+ /* "csamtools.pyx":3821
* pos = bam_tell( self.fp.x.bam )
* ret = samread( self.fp, b)
* if ret > 0: # <<<<<<<<<<<<<<
__pyx_t_4 = (__pyx_v_ret > 0);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":3822
+ /* "csamtools.pyx":3822
* ret = samread( self.fp, b)
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b )) # <<<<<<<<<<<<<<
* self.index[qname].append( pos )
*
*/
- __pyx_t_3 = __pyx_f_5pysam_9csamtools__charptr_to_str(bam1_qname(__pyx_v_b)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __pyx_f_9csamtools__charptr_to_str(bam1_qname(__pyx_v_b)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_qname);
__pyx_v_qname = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":3823
+ /* "csamtools.pyx":3823
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b ))
* self.index[qname].append( pos ) # <<<<<<<<<<<<<<
*
* bam_destroy1( b )
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __Pyx_PyInt_to_py_uint64_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
}
- /* "pysam/csamtools.pyx":3825
+ /* "csamtools.pyx":3825
* self.index[qname].append( pos )
*
* bam_destroy1( b ) # <<<<<<<<<<<<<<
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("pysam.csamtools.IndexedReads.build", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IndexedReads.build", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qname);
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static char __pyx_doc_5pysam_9csamtools_12IndexedReads_4find[] = "IndexedReads.find(self, qname)";
-static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("find (wrapper)", 0);
- __pyx_r = __pyx_pf_5pysam_9csamtools_12IndexedReads_4find(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "pysam/csamtools.pyx":3827
+/* "csamtools.pyx":3827
* bam_destroy1( b )
*
* def find( self, qname ): # <<<<<<<<<<<<<<
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_4find(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname) {
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static char __pyx_doc_9csamtools_12IndexedReads_2find[] = "IndexedReads.find(self, qname)";
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("find", 0);
+ __Pyx_RefNannySetupContext("find");
__Pyx_TraceCall("find", __pyx_f[0], 3827);
- /* "pysam/csamtools.pyx":3828
+ /* "csamtools.pyx":3828
*
* def find( self, qname ):
* if qname in self.index: # <<<<<<<<<<<<<<
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
* else:
*/
- __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_qname, __pyx_v_self->index, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PySequence_Contains(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":3829
+ /* "csamtools.pyx":3829
* def find( self, qname ):
* if qname in self.index:
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False ) # <<<<<<<<<<<<<<
* raise KeyError( "read %s not found" % qname )
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self->samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_4);
if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
- /* "pysam/csamtools.pyx":3831
+ /* "csamtools.pyx":3831
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
* else:
* raise KeyError( "read %s not found" % qname ) # <<<<<<<<<<<<<<
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_186), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.IndexedReads.find", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IndexedReads.find", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
-/* "pysam/csamtools.pyx":3833
+/* "csamtools.pyx":3833
* raise KeyError( "read %s not found" % qname )
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
*
*/
-static void __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self) {
+static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 3833);
- /* "pysam/csamtools.pyx":3834
+ /* "csamtools.pyx":3834
*
* def __dealloc__(self):
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* __all__ = ["Samfile",
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile __pyx_vtable_5pysam_9csamtools_Fastafile;
+static struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_Fastafile *p;
+static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Fastafile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Fastafile;
- if (__pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_Fastafile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
+ if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_Fastafile(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_9Fastafile_11__dealloc__(o);
+ __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastafile_filename(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_Fastafile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_2_isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_6_open)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_8close)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_12fetch)},
+static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Fastafile[] = {
- {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
{0, 0, 0, 0, 0}
};
};
static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
- __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*sq_length*/
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
};
static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*mp_length*/
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
+static PyTypeObject __pyx_type_9csamtools_Fastafile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.Fastafile"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_Fastafile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_Fastafile, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_Fastafile, /*tp_methods*/
+ __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_Fastafile, /*tp_getset*/
+ __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_Fastafile, /*tp_new*/
+ __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_AlignedRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_AlignedRead(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(o);
+ __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_query(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qend(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aend(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_alen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_positions(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_AlignedRead[] = {
- {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_6compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_10overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_12opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_14fancy_str)},
+static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
+ {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)},
+ {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)},
+ {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)},
+ {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_AlignedRead[] = {
- {(char *)"qname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0},
- {(char *)"cigar", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0},
- {(char *)"cigarstring", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0},
- {(char *)"seq", __pyx_getprop_5pysam_9csamtools_11AlignedRead_seq, __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0},
- {(char *)"qual", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qual, __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0},
- {(char *)"query", __pyx_getprop_5pysam_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0},
- {(char *)"qqual", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0},
- {(char *)"qstart", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0},
- {(char *)"qend", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0},
- {(char *)"qlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
- {(char *)"tags", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tags, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0},
- {(char *)"flag", __pyx_getprop_5pysam_9csamtools_11AlignedRead_flag, __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0},
- {(char *)"rname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0},
- {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tid, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
- {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0},
- {(char *)"bin", __pyx_getprop_5pysam_9csamtools_11AlignedRead_bin, __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0},
- {(char *)"rlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0},
- {(char *)"aend", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
- {(char *)"alen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
- {(char *)"mapq", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0},
- {(char *)"mrnm", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0},
- {(char *)"rnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0},
- {(char *)"mpos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0},
- {(char *)"pnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0},
- {(char *)"isize", __pyx_getprop_5pysam_9csamtools_11AlignedRead_isize, __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0},
- {(char *)"tlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0},
- {(char *)"is_paired", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0},
- {(char *)"is_proper_pair", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0},
- {(char *)"is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0},
- {(char *)"mate_is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0},
- {(char *)"is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0},
- {(char *)"mate_is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0},
- {(char *)"is_read1", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0},
- {(char *)"is_read2", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0},
- {(char *)"is_secondary", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0},
- {(char *)"is_qcfail", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0},
- {(char *)"is_duplicate", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0},
- {(char *)"positions", __pyx_getprop_5pysam_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
- {(char *)"aligned_pairs", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = {
+ {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0},
+ {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0},
+ {(char *)"cigarstring", __pyx_getprop_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0},
+ {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0},
+ {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0},
+ {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0},
+ {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0},
+ {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0},
+ {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0},
+ {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
+ {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0},
+ {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0},
+ {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0},
+ {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0},
+ {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0},
+ {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
+ {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
+ {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0},
+ {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0},
+ {(char *)"rnext", __pyx_getprop_9csamtools_11AlignedRead_rnext, __pyx_setprop_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0},
+ {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0},
+ {(char *)"pnext", __pyx_getprop_9csamtools_11AlignedRead_pnext, __pyx_setprop_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0},
+ {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0},
+ {(char *)"tlen", __pyx_getprop_9csamtools_11AlignedRead_tlen, __pyx_setprop_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0},
+ {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0},
+ {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0},
+ {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0},
+ {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0},
+ {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0},
+ {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0},
+ {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0},
+ {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0},
+ {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0},
+ {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0},
+ {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0},
+ {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
+ {(char *)"aligned_pairs", __pyx_getprop_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
{0, 0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_AlignedRead = {
+static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.AlignedRead"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_AlignedRead), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.AlignedRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_AlignedRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_AlignedRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_number_AlignedRead, /*tp_as_number*/
&__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
&__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
+ __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__, /*tp_str*/
+ __pyx_pf_9csamtools_11AlignedRead_2__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_AlignedRead, /*tp_methods*/
+ __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_AlignedRead, /*tp_getset*/
+ __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_AlignedRead, /*tp_new*/
+ __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile __pyx_vtable_5pysam_9csamtools_Samfile;
+static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *p;
+static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Samfile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Samfile;
- if (__pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_Samfile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
+ if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(o);
+ __pyx_pf_9csamtools_7Samfile_15__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_nreferences(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_references(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_lengths(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_mapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_text(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_header(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_2_isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_4_hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_6_open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_8gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_10getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_12_parseRegion)},
- {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_14reset)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_16seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_18tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_20fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_22mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_24count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_26pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_28close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_32write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_34__enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_36__exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_38_buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_42__next__)},
+static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)},
+ {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Samfile[] = {
- {(char *)"filename", __pyx_getprop_5pysam_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
- {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
- {(char *)"references", __pyx_getprop_5pysam_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
- {(char *)"lengths", __pyx_getprop_5pysam_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
- {(char *)"mapped", __pyx_getprop_5pysam_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
- {(char *)"unmapped", __pyx_getprop_5pysam_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
- {(char *)"text", __pyx_getprop_5pysam_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
- {(char *)"header", __pyx_getprop_5pysam_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
+ {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
+ {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
+ {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
+ {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
+ {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
+ {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
+ {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
{0, 0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
+static PyTypeObject __pyx_type_9csamtools_Samfile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.Samfile"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_Samfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_Samfile, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_7Samfile_41__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_7Samfile_43__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_Samfile, /*tp_methods*/
+ __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_Samfile, /*tp_getset*/
+ __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_Samfile, /*tp_new*/
+ __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupProxy(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_tid(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(o, v);
+ return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupProxy[] = {
+static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupProxy[] = {
- {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
- {(char *)"n", __pyx_getprop_5pysam_9csamtools_11PileupProxy_n, __pyx_setprop_5pysam_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0},
- {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pos, 0, 0, 0},
- {(char *)"pileups", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
+ {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
{0, 0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = {
+static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.PileupProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_PileupProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__, /*tp_str*/
+ __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_PileupProxy, /*tp_methods*/
+ __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_PileupProxy, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_PileupProxy, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p;
+static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_PileupRead *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_PileupRead *)o);
- p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_9csamtools_PileupRead *)o);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
- Py_CLEAR(p->_alignment);
+static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ Py_XDECREF(((PyObject *)p->_alignment));
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
if (p->_alignment) {
e = (*v)(((PyObject*)p->_alignment), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
+static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
PyObject* tmp;
tmp = ((PyObject*)p->_alignment);
- p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_alignment(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_qpos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_indel(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_del(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_head(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_level(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupRead[] = {
+static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupRead[] = {
- {(char *)"alignment", __pyx_getprop_5pysam_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
- {(char *)"qpos", __pyx_getprop_5pysam_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
- {(char *)"indel", __pyx_getprop_5pysam_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
- {(char *)"is_del", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
- {(char *)"is_head", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_head, 0, 0, 0},
- {(char *)"is_tail", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail, 0, 0, 0},
- {(char *)"level", __pyx_getprop_5pysam_9csamtools_10PileupRead_level, 0, 0, 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
+ {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
+ {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
+ {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
+ {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
+ {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
+ {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
+ {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
{0, 0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_PileupRead = {
+static PyTypeObject __pyx_type_9csamtools_PileupRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.PileupRead"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_PileupRead), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_PileupRead, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_9csamtools_10PileupRead_3__str__, /*tp_str*/
+ __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_PileupRead, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_PileupRead, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_PileupRead, /*tp_methods*/
+ __pyx_methods_9csamtools_PileupRead, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_PileupRead, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_PileupRead, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRow(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRow[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRow"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRow), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRow, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRow, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRow, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRow, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion __pyx_vtable_5pysam_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(o);
+ __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_CLEAR(p->samfile);
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+ Py_XDECREF(((PyObject *)p->samfile));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
- e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion)); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between\n samfile and the iterator.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowRegion, /*tp_methods*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll __pyx_vtable_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAll *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
- if (__pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
+ if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowAll"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowAll, /*tp_methods*/
+ __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowAll, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
- Py_CLEAR(p->samfile);
- Py_CLEAR(p->rowiter);
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->rowiter));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
- e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs)); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->rowiter);
- p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs, /*tp_methods*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection __pyx_vtable_5pysam_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+ p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
p->positions = Py_None; Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(o);
+ __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_CLEAR(p->positions);
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+ Py_XDECREF(p->positions);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
- e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection)); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->positions) {
e = (*v)(p->positions, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
tmp = ((PyObject*)p->positions);
p->positions = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowSelection"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowSelection, /*tp_methods*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowSelection, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_vtable_5pysam_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p;
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
- p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
p->stepper = Py_None; Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_CLEAR(p->iter);
- Py_CLEAR(p->samfile);
- Py_CLEAR(p->fastafile);
- Py_CLEAR(p->stepper);
+ Py_XDECREF(((PyObject *)p->iter));
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->fastafile));
+ Py_XDECREF(p->stepper);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
if (p->iter) {
e = (*v)(((PyObject*)p->iter), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
PyObject* tmp;
tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->fastafile);
- p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->stepper);
p->stepper = Py_None; Py_INCREF(Py_None);
return 0;
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_4addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_6hasReference)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
+ {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
+ {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
+ {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
{0, 0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorColumn"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumn), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n\n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns,\n but each object in ``result`` will contain the same information.\n\n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controls how the iterator advances.\n Possible options for the stepper are\n\n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n\n The default is to use \"all\" if no stepper is given.\n\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorColumn, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_IteratorColumn, /*tp_getset*/
+ __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorColumn, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
- if (__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
+ if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorColumnRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
- #else
0, /*tp_iter*/
- #endif
- __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorColumnRegion, /*tp_methods*/
+ __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
+ if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorColumnAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
- #else
0, /*tp_iter*/
- #endif
- __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
+ __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IndexedReads(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p;
+static PyObject *__pyx_tp_new_9csamtools_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IndexedReads *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_9csamtools_IndexedReads *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
p->index = Py_None; Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(o);
+ __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_CLEAR(p->samfile);
- Py_CLEAR(p->index);
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(p->index);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IndexedReads(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
PyObject* tmp;
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->index);
p->index = Py_None; Py_INCREF(Py_None);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IndexedReads[] = {
- {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_2build)},
- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_4find)},
+static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
+ {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)},
+ {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)},
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = {
+static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IndexedReads"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IndexedReads), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IndexedReads, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IndexedReads, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IndexedReads, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IndexedReads, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IndexedReads, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IndexedReads, /*tp_methods*/
+ __pyx_methods_9csamtools_IndexedReads, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IndexedReads, /*tp_new*/
+ __pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_SNPCall(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_SNPCall(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_tid(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_pos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_genotype(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_consensus_quality(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_coverage(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_SNPCall[] = {
+static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_SNPCall[] = {
- {(char *)"tid", __pyx_getprop_5pysam_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
- {(char *)"pos", __pyx_getprop_5pysam_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
- {(char *)"reference_base", __pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
- {(char *)"genotype", __pyx_getprop_5pysam_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
- {(char *)"consensus_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
- {(char *)"snp_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
- {(char *)"mapping_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
- {(char *)"coverage", __pyx_getprop_5pysam_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
+ {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
+ {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
+ {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
+ {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
+ {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
+ {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
{0, 0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
+static PyTypeObject __pyx_type_9csamtools_SNPCall = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.SNPCall"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_SNPCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_SNPCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_9csamtools_7SNPCall_1__str__, /*tp_str*/
+ __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_SNPCall, /*tp_methods*/
+ __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_SNPCall, /*tp_getset*/
+ __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_SNPCall, /*tp_new*/
+ __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p;
+static PyObject *__pyx_tp_new_9csamtools___pyx_Generator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_Generator_object *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o);
+ p = ((struct __pyx_Generator_object *)o);
+ p->exc_type = 0;
+ p->exc_value = 0;
+ p->exc_traceback = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools___pyx_Generator(PyObject *o) {
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ Py_XDECREF(p->exc_type);
+ Py_XDECREF(p->exc_value);
+ Py_XDECREF(p->exc_traceback);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools___pyx_Generator(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ if (p->exc_type) {
+ e = (*v)(p->exc_type, a); if (e) return e;
+ }
+ if (p->exc_value) {
+ e = (*v)(p->exc_value, a); if (e) return e;
+ }
+ if (p->exc_traceback) {
+ e = (*v)(p->exc_traceback, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools___pyx_Generator(PyObject *o) {
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->exc_type);
+ p->exc_type = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->exc_value);
+ p->exc_value = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->exc_traceback);
+ p->exc_traceback = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools___pyx_Generator[] = {
+ {__Pyx_NAMESTR("send"), (PyCFunction)__Pyx_Generator_Send, METH_O, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__Pyx_Generator_Close, METH_NOARGS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("throw"), (PyCFunction)__Pyx_Generator_Throw, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_Generator = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_Generator = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_Generator = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_Generator = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_Generator_type = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.__pyx_Generator"), /*tp_name*/
+ sizeof(struct __pyx_Generator_object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools___pyx_Generator, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_Generator, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_Generator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_Generator, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_Generator, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_9csamtools___pyx_Generator, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_Generator, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ PyObject_SelfIter, /*tp_iter*/
+ __Pyx_Generator_Next, /*tp_iternext*/
+ __pyx_methods_9csamtools___pyx_Generator, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools___pyx_Generator, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p;
+ PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o);
p->__pyx_v_x = 0;
p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
- Py_CLEAR(p->__pyx_v_x);
- Py_CLEAR(p->__pyx_v_y);
- Py_CLEAR(p->__pyx_t_0);
- Py_CLEAR(p->__pyx_t_1);
- (*Py_TYPE(o)->tp_free)(o);
+static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+ Py_XDECREF(p->__pyx_v_x);
+ Py_XDECREF(p->__pyx_v_y);
+ Py_XDECREF(p->__pyx_t_0);
+ Py_XDECREF(p->__pyx_t_1);
+ __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+ e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e;
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
+static int __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
PyObject* tmp;
+ __pyx_tp_clear_9csamtools___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr[] = {
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct__genexpr[] = {
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer___pyx_scope_struct__genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
+ __pyx_methods_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
+ __pyx_tp_new_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p;
+ PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o);
+ p = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o);
p->__pyx_v_x = 0;
p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
- Py_CLEAR(p->__pyx_v_x);
- Py_CLEAR(p->__pyx_v_y);
- Py_CLEAR(p->__pyx_t_0);
- Py_CLEAR(p->__pyx_t_1);
- (*Py_TYPE(o)->tp_free)(o);
+static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ Py_XDECREF(p->__pyx_v_x);
+ Py_XDECREF(p->__pyx_v_y);
+ Py_XDECREF(p->__pyx_t_0);
+ Py_XDECREF(p->__pyx_t_1);
+ __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e;
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+static int __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
PyObject* tmp;
+ __pyx_tp_clear_9csamtools___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr[] = {
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr[] = {
{0, 0, 0, 0}
};
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr = {
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
&__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
+ __pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
{&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
{&__pyx_n_s_249, __pyx_k_249, sizeof(__pyx_k_249), 0, 0, 1, 1},
{&__pyx_kp_s_251, __pyx_k_251, sizeof(__pyx_k_251), 0, 0, 1, 0},
+ {&__pyx_kp_s_254, __pyx_k_254, sizeof(__pyx_k_254), 0, 0, 1, 0},
+ {&__pyx_kp_s_255, __pyx_k_255, sizeof(__pyx_k_255), 0, 0, 1, 0},
{&__pyx_kp_s_256, __pyx_k_256, sizeof(__pyx_k_256), 0, 0, 1, 0},
- {&__pyx_n_s_257, __pyx_k_257, sizeof(__pyx_k_257), 0, 0, 1, 1},
- {&__pyx_kp_s_258, __pyx_k_258, sizeof(__pyx_k_258), 0, 0, 1, 0},
- {&__pyx_kp_s_267, __pyx_k_267, sizeof(__pyx_k_267), 0, 0, 1, 0},
- {&__pyx_kp_s_274, __pyx_k_274, sizeof(__pyx_k_274), 0, 0, 1, 0},
+ {&__pyx_kp_s_262, __pyx_k_262, sizeof(__pyx_k_262), 0, 0, 1, 0},
{&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
- {&__pyx_kp_s_291, __pyx_k_291, sizeof(__pyx_k_291), 0, 0, 1, 0},
{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
{&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
{&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
{&__pyx_n_s___open, __pyx_k___open, sizeof(__pyx_k___open), 0, 0, 1, 1},
{&__pyx_n_s___parseRegion, __pyx_k___parseRegion, sizeof(__pyx_k___parseRegion), 0, 0, 1, 1},
{&__pyx_n_s___samtools_dispatch, __pyx_k___samtools_dispatch, sizeof(__pyx_k___samtools_dispatch), 0, 0, 1, 1},
- {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1},
{&__pyx_n_s__add_sq_text, __pyx_k__add_sq_text, sizeof(__pyx_k__add_sq_text), 0, 0, 1, 1},
{&__pyx_n_s__alignment, __pyx_k__alignment, sizeof(__pyx_k__alignment), 0, 0, 1, 1},
{&__pyx_n_s__all, __pyx_k__all, sizeof(__pyx_k__all), 0, 0, 1, 1},
{&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1},
{&__pyx_n_s__calcsize, __pyx_k__calcsize, sizeof(__pyx_k__calcsize), 0, 0, 1, 1},
{&__pyx_n_s__callback, __pyx_k__callback, sizeof(__pyx_k__callback), 0, 0, 1, 1},
- {&__pyx_n_s__cargs, __pyx_k__cargs, sizeof(__pyx_k__cargs), 0, 0, 1, 1},
{&__pyx_n_s__catch_stdout, __pyx_k__catch_stdout, sizeof(__pyx_k__catch_stdout), 0, 0, 1, 1},
{&__pyx_n_s__check_header, __pyx_k__check_header, sizeof(__pyx_k__check_header), 0, 0, 1, 1},
{&__pyx_n_s__check_sq, __pyx_k__check_sq, sizeof(__pyx_k__check_sq), 0, 0, 1, 1},
{&__pyx_n_s__compile, __pyx_k__compile, sizeof(__pyx_k__compile), 0, 0, 1, 1},
{&__pyx_n_s__consensus_quality, __pyx_k__consensus_quality, sizeof(__pyx_k__consensus_quality), 0, 0, 1, 1},
{&__pyx_n_s__coverage, __pyx_k__coverage, sizeof(__pyx_k__coverage), 0, 0, 1, 1},
+ {&__pyx_n_s__csamtools, __pyx_k__csamtools, sizeof(__pyx_k__csamtools), 0, 0, 1, 1},
{&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1},
{&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1},
{&__pyx_n_s__data_len, __pyx_k__data_len, sizeof(__pyx_k__data_len), 0, 0, 1, 1},
{&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1},
{&__pyx_n_s__indel, __pyx_k__indel, sizeof(__pyx_k__indel), 0, 0, 1, 1},
{&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1},
- {&__pyx_n_s__inf, __pyx_k__inf, sizeof(__pyx_k__inf), 0, 0, 1, 1},
{&__pyx_n_s__is_del, __pyx_k__is_del, sizeof(__pyx_k__is_del), 0, 0, 1, 1},
{&__pyx_n_s__is_head, __pyx_k__is_head, sizeof(__pyx_k__is_head), 0, 0, 1, 1},
{&__pyx_n_s__is_tail, __pyx_k__is_tail, sizeof(__pyx_k__is_tail), 0, 0, 1, 1},
{&__pyx_n_s__nextiter, __pyx_k__nextiter, sizeof(__pyx_k__nextiter), 0, 0, 1, 1},
{&__pyx_n_s__nreferences, __pyx_k__nreferences, sizeof(__pyx_k__nreferences), 0, 0, 1, 1},
{&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1},
- {&__pyx_n_s__ofd, __pyx_k__ofd, sizeof(__pyx_k__ofd), 0, 0, 1, 1},
{&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1},
{&__pyx_n_s__open, __pyx_k__open, sizeof(__pyx_k__open), 0, 0, 1, 1},
{&__pyx_n_s__ord, __pyx_k__ord, sizeof(__pyx_k__ord), 0, 0, 1, 1},
{&__pyx_n_s__os, __pyx_k__os, sizeof(__pyx_k__os), 0, 0, 1, 1},
- {&__pyx_n_s__out_stderr, __pyx_k__out_stderr, sizeof(__pyx_k__out_stderr), 0, 0, 1, 1},
- {&__pyx_n_s__out_stdout, __pyx_k__out_stdout, sizeof(__pyx_k__out_stdout), 0, 0, 1, 1},
{&__pyx_n_s__pack_into, __pyx_k__pack_into, sizeof(__pyx_k__pack_into), 0, 0, 1, 1},
{&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1},
{&__pyx_n_s__pileups, __pyx_k__pileups, sizeof(__pyx_k__pileups), 0, 0, 1, 1},
{&__pyx_n_s__remove, __pyx_k__remove, sizeof(__pyx_k__remove), 0, 0, 1, 1},
{&__pyx_n_s__reopen, __pyx_k__reopen, sizeof(__pyx_k__reopen), 0, 0, 1, 1},
{&__pyx_n_s__restore, __pyx_k__restore, sizeof(__pyx_k__restore), 0, 0, 1, 1},
- {&__pyx_n_s__retval, __pyx_k__retval, sizeof(__pyx_k__retval), 0, 0, 1, 1},
{&__pyx_n_s__rlen, __pyx_k__rlen, sizeof(__pyx_k__rlen), 0, 0, 1, 1},
{&__pyx_n_s__rname, __pyx_k__rname, sizeof(__pyx_k__rname), 0, 0, 1, 1},
{&__pyx_n_s__s, __pyx_k__s, sizeof(__pyx_k__s), 0, 0, 1, 1},
{&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1},
{&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
{&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1},
- {&__pyx_n_s__stderr_f, __pyx_k__stderr_f, sizeof(__pyx_k__stderr_f), 0, 0, 1, 1},
- {&__pyx_n_s__stderr_h, __pyx_k__stderr_h, sizeof(__pyx_k__stderr_h), 0, 0, 1, 1},
{&__pyx_n_s__stdout, __pyx_k__stdout, sizeof(__pyx_k__stdout), 0, 0, 1, 1},
- {&__pyx_n_s__stdout_f, __pyx_k__stdout_f, sizeof(__pyx_k__stdout_f), 0, 0, 1, 1},
- {&__pyx_n_s__stdout_h, __pyx_k__stdout_h, sizeof(__pyx_k__stdout_h), 0, 0, 1, 1},
- {&__pyx_n_s__stdout_save, __pyx_k__stdout_save, sizeof(__pyx_k__stdout_save), 0, 0, 1, 1},
{&__pyx_n_s__stepper, __pyx_k__stepper, sizeof(__pyx_k__stepper), 0, 0, 1, 1},
{&__pyx_n_s__streams, __pyx_k__streams, sizeof(__pyx_k__streams), 0, 0, 1, 1},
{&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1},
static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
+ __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants");
- /* "pysam/csamtools.pyx":64
+ /* "csamtools.pyx":64
* return s
* elif PyUnicode_Check(s):
* return s.encode('ascii') # <<<<<<<<<<<<<<
* raise TypeError, u"Argument must be string, bytes or unicode."
*/
__pyx_k_tuple_2 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_2));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_2, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
- /* "pysam/csamtools.pyx":84
+ /* "csamtools.pyx":84
* return s
* elif PyBytes_Check(s):
* return s.decode('ascii') # <<<<<<<<<<<<<<
* # assume unicode
*/
__pyx_k_tuple_4 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_4));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
- /* "pysam/csamtools.pyx":398
+ /* "csamtools.pyx":398
* def __len__(self):
* if self.fastafile == NULL:
* raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
* return faidx_fetch_nseq(self.fastafile)
*/
__pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_8));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_8));
- /* "pysam/csamtools.pyx":431
+ /* "csamtools.pyx":431
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_11);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_11));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
- /* "pysam/csamtools.pyx":456
+ /* "csamtools.pyx":456
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* cdef int length
*/
__pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_12);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_12));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
- /* "pysam/csamtools.pyx":462
+ /* "csamtools.pyx":462
*
* if not region:
* if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
* if end is None: end = max_pos -1
*/
__pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_14);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_14));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_13));
PyTuple_SET_ITEM(__pyx_k_tuple_14, 0, ((PyObject *)__pyx_kp_s_13));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_13));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
- /* "pysam/csamtools.pyx":481
+ /* "csamtools.pyx":481
* region = "%s:%i-%i" % (reference, start+1, end)
* if PY_MAJOR_VERSION >= 3:
* region = region.encode('ascii') # <<<<<<<<<<<<<<
* region,
*/
__pyx_k_tuple_20 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_20);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_20));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
- /* "pysam/csamtools.pyx":663
+ /* "csamtools.pyx":663
* if self._filename != NULL: free(self._filename )
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<<
* #cfilename = filename.encode(_FILENAME_ENCODING)
*/
__pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_25);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_25));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_25, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_25));
- /* "pysam/csamtools.pyx":790
+ /* "csamtools.pyx":790
* returns -1 if reference is not known.
* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return pysam_reference2tid( self.samfile.header, reference )
*/
__pyx_k_tuple_39 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_39);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_39));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_39, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));
- /* "pysam/csamtools.pyx":797
+ /* "csamtools.pyx":797
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
__pyx_k_tuple_40 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_40);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_40));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_40, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
- /* "pysam/csamtools.pyx":805
+ /* "csamtools.pyx":805
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
__pyx_k_tuple_42 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_42);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_42));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_42, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
- /* "pysam/csamtools.pyx":855
+ /* "csamtools.pyx":855
* if len(parts) >= 3: rend = int(parts[2])
*
* if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
* rtid = self.gettid( reference )
*/
__pyx_k_tuple_44 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_44);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_44));
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
- /* "pysam/csamtools.pyx":875
+ /* "csamtools.pyx":875
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* raise NotImplementedError("seek only available in bam files")
*/
__pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_47);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_47));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
- /* "pysam/csamtools.pyx":877
+ /* "csamtools.pyx":877
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
* raise OSError("seek no available in streams")
*/
__pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_49);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_49));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
PyTuple_SET_ITEM(__pyx_k_tuple_49, 0, ((PyObject *)__pyx_kp_s_48));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
- /* "pysam/csamtools.pyx":879
+ /* "csamtools.pyx":879
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
* raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
* return bam_seek( self.samfile.x.bam, offset, where )
*/
__pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_51);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_51));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_50));
PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_50));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_50));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
- /* "pysam/csamtools.pyx":888
+ /* "csamtools.pyx":888
* '''
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* raise NotImplementedError("seek only available in bam files")
*/
__pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_52);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_52));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
- /* "pysam/csamtools.pyx":890
+ /* "csamtools.pyx":890
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
* return bam_tell( self.samfile.x.bam )
*/
__pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_53);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_53));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_48));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
- /* "pysam/csamtools.pyx":925
+ /* "csamtools.pyx":925
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
__pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_55);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_55));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
- /* "pysam/csamtools.pyx":934
+ /* "csamtools.pyx":934
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
* if callback:
*/
__pyx_k_tuple_57 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_57);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_57));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, ((PyObject *)__pyx_kp_s_56));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
- /* "pysam/csamtools.pyx":937
+ /* "csamtools.pyx":937
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* return bam_fetch(self.samfile.x.bam,
*/
__pyx_k_tuple_59 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_59);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_59));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
PyTuple_SET_ITEM(__pyx_k_tuple_59, 0, ((PyObject *)__pyx_kp_s_58));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));
- /* "pysam/csamtools.pyx":938
+ /* "csamtools.pyx":938
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* self.index,
*/
__pyx_k_tuple_61 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_61);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_61));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
PyTuple_SET_ITEM(__pyx_k_tuple_61, 0, ((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
- /* "pysam/csamtools.pyx":957
+ /* "csamtools.pyx":957
* else:
* if has_coord:
* raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
* if callback:
*/
__pyx_k_tuple_63 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_63);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_63));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_62));
PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_kp_s_62));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_62));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
- /* "pysam/csamtools.pyx":960
+ /* "csamtools.pyx":960
*
* if callback:
* raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
* if self.samfile.header == NULL:
*/
__pyx_k_tuple_65 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_65);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_65));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_64));
PyTuple_SET_ITEM(__pyx_k_tuple_65, 0, ((PyObject *)__pyx_kp_s_64));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_64));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65));
- /* "pysam/csamtools.pyx":963
+ /* "csamtools.pyx":963
*
* if self.samfile.header == NULL:
* raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
* # check if targets are defined
*/
__pyx_k_tuple_67 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_67);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_67));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
PyTuple_SET_ITEM(__pyx_k_tuple_67, 0, ((PyObject *)__pyx_kp_s_66));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67));
- /* "pysam/csamtools.pyx":968
+ /* "csamtools.pyx":968
* # give warning, sam_read1 segfaults
* if self.samfile.header.n_targets == 0:
* warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<<
* return IteratorRowAll( self, reopen=reopen )
*/
__pyx_k_tuple_68 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_68);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_68));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_kp_s_66));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));
- /* "pysam/csamtools.pyx":1009
+ /* "csamtools.pyx":1009
*
* if mate_data.mate == NULL:
* raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
__pyx_k_tuple_72 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_72);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_72));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_71));
PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_kp_s_71));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_71));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
- /* "pysam/csamtools.pyx":1034
+ /* "csamtools.pyx":1034
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
__pyx_k_tuple_74 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_74);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_74));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74));
- /* "pysam/csamtools.pyx":1043
+ /* "csamtools.pyx":1043
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
* if not region:
*/
__pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_75);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_75));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_kp_s_56));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
- /* "pysam/csamtools.pyx":1046
+ /* "csamtools.pyx":1046
*
* if not region:
* raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
*/
__pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_77);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_77));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
- /* "pysam/csamtools.pyx":1047
+ /* "csamtools.pyx":1047
* if not region:
* raise ValueError( "counting functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* self.index,
*/
__pyx_k_tuple_78 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_78);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_78));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
- /* "pysam/csamtools.pyx":1057
+ /* "csamtools.pyx":1057
* return counter
* else:
* raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
* def pileup( self,
*/
__pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_80);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_80));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_79));
PyTuple_SET_ITEM(__pyx_k_tuple_80, 0, ((PyObject *)__pyx_kp_s_79));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_79));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
- /* "pysam/csamtools.pyx":1116
+ /* "csamtools.pyx":1116
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
__pyx_k_tuple_81 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_81);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_81));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_81, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_81));
- /* "pysam/csamtools.pyx":1121
+ /* "csamtools.pyx":1121
*
* if self.isbam:
* if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
* if callback:
*/
__pyx_k_tuple_83 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_83);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_83));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_82));
PyTuple_SET_ITEM(__pyx_k_tuple_83, 0, ((PyObject *)__pyx_kp_s_82));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_82));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83));
- /* "pysam/csamtools.pyx":1124
+ /* "csamtools.pyx":1124
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback )
*/
__pyx_k_tuple_84 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_84);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_84));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
PyTuple_SET_ITEM(__pyx_k_tuple_84, 0, ((PyObject *)__pyx_kp_s_58));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_84));
- /* "pysam/csamtools.pyx":1145
+ /* "csamtools.pyx":1145
*
* else:
* raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
* def close( self ):
*/
__pyx_k_tuple_86 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_86);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_86));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_85));
PyTuple_SET_ITEM(__pyx_k_tuple_86, 0, ((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
- /* "pysam/csamtools.pyx":1189
+ /* "csamtools.pyx":1189
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_87 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_87);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_87));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_87, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
- /* "pysam/csamtools.pyx":1195
+ /* "csamtools.pyx":1195
* '''number of :term:`reference` sequences in the file.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_88 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_88);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_88));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_88, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_88));
- /* "pysam/csamtools.pyx":1201
+ /* "csamtools.pyx":1201
* """tuple with the names of :term:`reference` sequences."""
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* for x from 0 <= x < self.samfile.header.n_targets:
*/
__pyx_k_tuple_89 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_89);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_89));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_89, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89));
- /* "pysam/csamtools.pyx":1212
+ /* "csamtools.pyx":1212
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* for x from 0 <= x < self.samfile.header.n_targets:
*/
__pyx_k_tuple_90 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_90)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_90);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_90));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_90, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_90));
- /* "pysam/csamtools.pyx":1222
+ /* "csamtools.pyx":1222
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_91 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_91);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_91));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_91, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_91));
- /* "pysam/csamtools.pyx":1223
+ /* "csamtools.pyx":1223
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
* cdef int tid
*/
__pyx_k_tuple_93 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_93)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_93);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_93));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_92));
PyTuple_SET_ITEM(__pyx_k_tuple_93, 0, ((PyObject *)__pyx_kp_s_92));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_93));
- /* "pysam/csamtools.pyx":1235
+ /* "csamtools.pyx":1235
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* cdef int tid
*/
__pyx_k_tuple_94 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_94)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_94);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_94));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_94, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_94));
- /* "pysam/csamtools.pyx":1236
+ /* "csamtools.pyx":1236
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
* cdef uint32_t total = 0
*/
__pyx_k_tuple_96 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_96);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_96));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_95));
PyTuple_SET_ITEM(__pyx_k_tuple_96, 0, ((PyObject *)__pyx_kp_s_95));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_95));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
- /* "pysam/csamtools.pyx":1248
+ /* "csamtools.pyx":1248
* '''full contents of the :term:`sam file` header as a string.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_97 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_97);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_97));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_97, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
- /* "pysam/csamtools.pyx":1256
+ /* "csamtools.pyx":1256
* '''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* result = {}
*/
__pyx_k_tuple_98 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_98);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_98));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_98, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
- /* "pysam/csamtools.pyx":1263
+ /* "csamtools.pyx":1263
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
* for line in t.split("\n"): # <<<<<<<<<<<<<<
* assert line.startswith("@"), "header line without '@': '%s'" % line
*/
__pyx_k_tuple_99 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_99);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_99));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
PyTuple_SET_ITEM(__pyx_k_tuple_99, 0, ((PyObject *)__pyx_kp_s_6));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
- /* "pysam/csamtools.pyx":1265
+ /* "csamtools.pyx":1265
* for line in t.split("\n"):
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
* record = fields[0]
*/
__pyx_k_tuple_101 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_101)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_101);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_101));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_100));
PyTuple_SET_ITEM(__pyx_k_tuple_101, 0, ((PyObject *)__pyx_kp_s_100));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_100));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_101));
- /* "pysam/csamtools.pyx":1266
+ /* "csamtools.pyx":1266
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t") # <<<<<<<<<<<<<<
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
*/
__pyx_k_tuple_103 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_103);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_103));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
PyTuple_SET_ITEM(__pyx_k_tuple_103, 0, ((PyObject *)__pyx_kp_s_5));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
- /* "pysam/csamtools.pyx":1279
+ /* "csamtools.pyx":1279
* x = {}
* for field in fields[1:]:
* key, value = field.split(":",1) # <<<<<<<<<<<<<<
* # lowercase are permitted for user fields
*/
__pyx_k_tuple_106 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_106)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_106);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_106));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_105));
PyTuple_SET_ITEM(__pyx_k_tuple_106, 0, ((PyObject *)__pyx_kp_s_105));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_105));
__Pyx_GIVEREF(__pyx_int_1);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_106));
- /* "pysam/csamtools.pyx":1377
+ /* "csamtools.pyx":1377
* dest.text = <char*>calloc( len(text), sizeof(char))
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_112 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_112);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_112));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_112, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112));
- /* "pysam/csamtools.pyx":1397
+ /* "csamtools.pyx":1397
* seqname, seqlen = seqs[x]
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<<
* dest.target_len[x] = seqlen
*/
__pyx_k_tuple_114 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_114)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_114);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_114));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_114, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_114));
- /* "pysam/csamtools.pyx":1412
+ /* "csamtools.pyx":1412
* ###############################################################
* def __iter__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* raise NotImplementedError( "can not iterate over samfile without header")
*/
__pyx_k_tuple_115 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_115)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_115);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_115));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_115, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_115));
- /* "pysam/csamtools.pyx":1414
+ /* "csamtools.pyx":1414
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_117 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_117);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_117));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_116));
PyTuple_SET_ITEM(__pyx_k_tuple_117, 0, ((PyObject *)__pyx_kp_s_116));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_116));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117));
- /* "pysam/csamtools.pyx":1484
+ /* "csamtools.pyx":1484
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not samfile._hasIndex():
*/
__pyx_k_tuple_118 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_118)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_118);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_118));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_118, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_118));
- /* "pysam/csamtools.pyx":1487
+ /* "csamtools.pyx":1487
*
* if not samfile._hasIndex():
* raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
* # makes sure that samfile stays alive as long as the
*/
__pyx_k_tuple_120 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_120);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_120));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_119));
PyTuple_SET_ITEM(__pyx_k_tuple_120, 0, ((PyObject *)__pyx_kp_s_119));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_119));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_120));
- /* "pysam/csamtools.pyx":1553
+ /* "csamtools.pyx":1553
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if samfile.isbam: mode = b"rb"
*/
__pyx_k_tuple_121 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_121)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_121);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_121));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_121, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_121));
- /* "pysam/csamtools.pyx":1604
+ /* "csamtools.pyx":1604
* def __cinit__(self, Samfile samfile):
* assert samfile._isOpen()
* if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
* self.tid = -1
*/
__pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_122);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_122));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
PyTuple_SET_ITEM(__pyx_k_tuple_122, 0, ((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
- /* "pysam/csamtools.pyx":1650
+ /* "csamtools.pyx":1650
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not samfile._isOpen():
*/
__pyx_k_tuple_123 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_123)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_123);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_123));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_123, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_123));
- /* "pysam/csamtools.pyx":1653
+ /* "csamtools.pyx":1653
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* assert samfile.isbam, "can only use this iterator on bam files"
*/
__pyx_k_tuple_124 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_124);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_124));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_124, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
- /* "pysam/csamtools.pyx":1954
+ /* "csamtools.pyx":1954
* self.cnext()
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
* if self.plp == NULL:
*/
__pyx_k_tuple_130 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_130)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_130);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_130));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
PyTuple_SET_ITEM(__pyx_k_tuple_130, 0, ((PyObject *)__pyx_kp_s_129));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_130));
- /* "pysam/csamtools.pyx":1990
+ /* "csamtools.pyx":1990
*
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
* # return result, if within same reference
*/
__pyx_k_tuple_131 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_131);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_131));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
PyTuple_SET_ITEM(__pyx_k_tuple_131, 0, ((PyObject *)__pyx_kp_s_129));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131));
- /* "pysam/csamtools.pyx":2153
+ /* "csamtools.pyx":2153
* qual = self.qual
* else:
* seq = self.seq.decode('ascii') # <<<<<<<<<<<<<<
* return "\t".join(map(str, (self.qname,
*/
__pyx_k_tuple_133 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_133);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_133));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_133, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_133));
- /* "pysam/csamtools.pyx":2154
+ /* "csamtools.pyx":2154
* else:
* seq = self.seq.decode('ascii')
* qual = self.qual.decode('ascii') # <<<<<<<<<<<<<<
* self.flag,
*/
__pyx_k_tuple_134 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_134)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_134);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_134));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_134, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_134));
- /* "pysam/csamtools.pyx":2563
+ /* "csamtools.pyx":2563
* for pytag, value in tags:
* if not type(pytag) is bytes:
* pytag = pytag.encode('ascii') # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_139 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_139);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_139));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_139, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_139));
- /* "pysam/csamtools.pyx":2591
+ /* "csamtools.pyx":2591
* datafmt = "2sccI%i%s" % (len(value), datafmt)
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* len(value)] + list(value) )
*/
__pyx_k_tuple_142 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_142)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_142);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_142));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_142, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_142));
- /* "pysam/csamtools.pyx":2592
+ /* "csamtools.pyx":2592
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
* datatype.encode('ascii'), # <<<<<<<<<<<<<<
* fmts.append( datafmt )
*/
__pyx_k_tuple_143 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_143)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_143);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_143));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_143, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_143));
- /* "pysam/csamtools.pyx":2615
+ /* "csamtools.pyx":2615
* # Note: hex strings (H) are not supported yet
* if t is not bytes:
* value = value.encode('ascii') # <<<<<<<<<<<<<<
* fmt, pytype = "2scc", 'A'
*/
__pyx_k_tuple_144 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_144)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_144);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_144));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_144, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_144));
- /* "pysam/csamtools.pyx":2622
+ /* "csamtools.pyx":2622
*
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_146 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_146)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_146);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_146));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_146, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_146));
- /* "pysam/csamtools.pyx":3020
+ /* "csamtools.pyx":3020
* '''
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
* def __str__(self):
*/
__pyx_k_tuple_172 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_172)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_172);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_172));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
PyTuple_SET_ITEM(__pyx_k_tuple_172, 0, ((PyObject *)__pyx_kp_s_171));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_172));
- /* "pysam/csamtools.pyx":3046
+ /* "csamtools.pyx":3046
*
* if self.plp[0] == NULL:
* raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<<
* # warning: there could be problems if self.n and self.buf are
*/
__pyx_k_tuple_174 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_174);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_174));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_173));
PyTuple_SET_ITEM(__pyx_k_tuple_174, 0, ((PyObject *)__pyx_kp_s_173));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_173));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_174));
- /* "pysam/csamtools.pyx":3059
+ /* "csamtools.pyx":3059
*
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
* def __str__(self):
*/
__pyx_k_tuple_175 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_175);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_175));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
PyTuple_SET_ITEM(__pyx_k_tuple_175, 0, ((PyObject *)__pyx_kp_s_171));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_175));
- /* "pysam/csamtools.pyx":3172
+ /* "csamtools.pyx":3172
* # recover. Thus redirect output to file with -o option.
* if method == "view":
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
*
*/
__pyx_k_tuple_180 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_180);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_180));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_179));
PyTuple_SET_ITEM(__pyx_k_tuple_180, 0, ((PyObject *)__pyx_kp_s_179));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_179));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_180));
- /* "pysam/csamtools.pyx":3197
+ /* "csamtools.pyx":3197
* stdout_save.restore()
* try:
* with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
*/
__pyx_k_tuple_181 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_181);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_181));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_181, 0, Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181));
- /* "pysam/csamtools.pyx":3200
+ /* "csamtools.pyx":3200
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
* out_stdout = inf.read()
*/
__pyx_k_tuple_182 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_182);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_182));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_182, 0, Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_182));
- /* "pysam/csamtools.pyx":3210
+ /* "csamtools.pyx":3210
* pysam_unset_stderr()
* try:
* with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
*/
__pyx_k_tuple_183 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_183);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_183));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_183, 0, Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_183));
- /* "pysam/csamtools.pyx":3213
+ /* "csamtools.pyx":3213
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
* out_stderr = inf.read()
*/
__pyx_k_tuple_184 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_184);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_184));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_184, 0, Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(Py_None);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_184));
- /* "pysam/csamtools.pyx":143
+ /* "csamtools.pyx":143
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
* CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) # <<<<<<<<<<<<<<
* #####################################################################
*/
__pyx_k_tuple_252 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_252);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_252));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_251));
PyTuple_SET_ITEM(__pyx_k_tuple_252, 0, ((PyObject *)__pyx_kp_s_251));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_251));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_252));
- /* "pysam/csamtools.pyx":260
- * list of reads (:class:`pysam.PileupRead`) aligned to this column
- * '''
- * def __str__(self): # <<<<<<<<<<<<<<
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" + "\n".join( map(str, self.pileups) )
- */
- __pyx_k_tuple_254 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_254);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_254, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_254));
- __pyx_k_codeobj_255 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_254, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____str__, 260, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":308
- * stderr is captured.
- * '''
- * def __init__(self): # <<<<<<<<<<<<<<
- * return
- * self.stderr_h, self.stderr_f = tempfile.mkstemp()
- */
- __pyx_k_tuple_259 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_259);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_259));
- __pyx_k_codeobj_260 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_259, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 308, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":314
- * self.stderr_save.setfd( self.stderr_h )
- *
- * def readAndRelease( self ): # <<<<<<<<<<<<<<
- * return []
- * self.stderr_save.restore()
- */
- __pyx_k_tuple_261 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_261)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_261);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_261, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_261));
- __pyx_k_codeobj_262 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_261, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__readAndRelease, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_262)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":323
- * return lines
- *
- * def release(self): # <<<<<<<<<<<<<<
- * return
- * self.stderr_save.restore()
- */
- __pyx_k_tuple_263 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_263)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_263);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_263, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_263));
- __pyx_k_codeobj_264 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_263, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__release, 323, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_264)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":329
- * os.remove( self.stderr_f )
- *
- * def __del__(self): # <<<<<<<<<<<<<<
- * self.release()
- *
- */
- __pyx_k_tuple_265 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_265)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_265);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_265, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_265));
- __pyx_k_codeobj_266 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_265, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____del__, 329, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_266)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":334
- * class StderrStoreWindows():
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass # <<<<<<<<<<<<<<
- * def readAndRelease(self): return []
- * def release(self): pass
- */
- __pyx_k_tuple_268 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_268)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_268);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_268, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_268));
- __pyx_k_codeobj_269 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_268, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 334, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_269)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":335
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass
- * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
- * def release(self): pass
- *
- */
- __pyx_k_tuple_270 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_270)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_270);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_270, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_270));
- __pyx_k_codeobj_271 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_270, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__readAndRelease, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_271)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":336
- * def __init__(self): pass
- * def readAndRelease(self): return []
- * def release(self): pass # <<<<<<<<<<<<<<
- *
- * if platform.system()=='Windows':
- */
- __pyx_k_tuple_272 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_272)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_272);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_272, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_272));
- __pyx_k_codeobj_273 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_272, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__release, 336, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_273)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":354
+ /* "csamtools.pyx":354
*
* # order of records within sam headers
* VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<<
*
* # type conversions within sam header records
*/
- __pyx_k_tuple_275 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_275)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_275);
+ __pyx_k_tuple_257 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_257));
__Pyx_INCREF(((PyObject *)__pyx_n_s__HD));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 0, ((PyObject *)__pyx_n_s__HD));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 0, ((PyObject *)__pyx_n_s__HD));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__HD));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SQ));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 1, ((PyObject *)__pyx_n_s__SQ));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 1, ((PyObject *)__pyx_n_s__SQ));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SQ));
__Pyx_INCREF(((PyObject *)__pyx_n_s__RG));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 2, ((PyObject *)__pyx_n_s__RG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 2, ((PyObject *)__pyx_n_s__RG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__RG));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 3, ((PyObject *)__pyx_n_s__PG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 3, ((PyObject *)__pyx_n_s__PG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CO));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 4, ((PyObject *)__pyx_n_s__CO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 4, ((PyObject *)__pyx_n_s__CO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CO));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_275));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_257));
- /* "pysam/csamtools.pyx":364
+ /* "csamtools.pyx":364
*
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
*/
- __pyx_k_tuple_276 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_276)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_276);
+ __pyx_k_tuple_258 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_258));
__Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 0, ((PyObject *)__pyx_n_s__VN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__VN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SO));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 1, ((PyObject *)__pyx_n_s__SO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 1, ((PyObject *)__pyx_n_s__SO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SO));
__Pyx_INCREF(((PyObject *)__pyx_n_s__GO));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 2, ((PyObject *)__pyx_n_s__GO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 2, ((PyObject *)__pyx_n_s__GO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__GO));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_276));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
- /* "pysam/csamtools.pyx":365
+ /* "csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*/
- __pyx_k_tuple_277 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_277)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_277);
+ __pyx_k_tuple_259 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_259));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SN));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 0, ((PyObject *)__pyx_n_s__SN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 0, ((PyObject *)__pyx_n_s__SN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__LN));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 1, ((PyObject *)__pyx_n_s__LN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 1, ((PyObject *)__pyx_n_s__LN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__LN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__AS));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 2, ((PyObject *)__pyx_n_s__AS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 2, ((PyObject *)__pyx_n_s__AS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__AS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__M5));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 3, ((PyObject *)__pyx_n_s__M5));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 3, ((PyObject *)__pyx_n_s__M5));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__M5));
__Pyx_INCREF(((PyObject *)__pyx_n_s__UR));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 4, ((PyObject *)__pyx_n_s__UR));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 4, ((PyObject *)__pyx_n_s__UR));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__UR));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SP));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 5, ((PyObject *)__pyx_n_s__SP));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 5, ((PyObject *)__pyx_n_s__SP));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SP));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_277));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_259));
- /* "pysam/csamtools.pyx":366
+ /* "csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<<
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*
*/
- __pyx_k_tuple_278 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_278)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_278);
+ __pyx_k_tuple_260 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_260));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 0, ((PyObject *)__pyx_n_s__ID));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 0, ((PyObject *)__pyx_n_s__ID));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SM));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 1, ((PyObject *)__pyx_n_s__SM));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 1, ((PyObject *)__pyx_n_s__SM));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SM));
__Pyx_INCREF(((PyObject *)__pyx_n_s__LB));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 2, ((PyObject *)__pyx_n_s__LB));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 2, ((PyObject *)__pyx_n_s__LB));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__LB));
__Pyx_INCREF(((PyObject *)__pyx_n_s__DS));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 3, ((PyObject *)__pyx_n_s__DS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 3, ((PyObject *)__pyx_n_s__DS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__DS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PU));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 4, ((PyObject *)__pyx_n_s__PU));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 4, ((PyObject *)__pyx_n_s__PU));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PU));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PI));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 5, ((PyObject *)__pyx_n_s__PI));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 5, ((PyObject *)__pyx_n_s__PI));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PI));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CN));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 6, ((PyObject *)__pyx_n_s__CN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 6, ((PyObject *)__pyx_n_s__CN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__DT));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 7, ((PyObject *)__pyx_n_s__DT));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 7, ((PyObject *)__pyx_n_s__DT));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__DT));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PL));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 8, ((PyObject *)__pyx_n_s__PL));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 8, ((PyObject *)__pyx_n_s__PL));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PL));
__Pyx_INCREF(((PyObject *)__pyx_n_s__FO));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 9, ((PyObject *)__pyx_n_s__FO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 9, ((PyObject *)__pyx_n_s__FO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__FO));
__Pyx_INCREF(((PyObject *)__pyx_n_s__KS));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 10, ((PyObject *)__pyx_n_s__KS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 10, ((PyObject *)__pyx_n_s__KS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__KS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 11, ((PyObject *)__pyx_n_s__PG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 11, ((PyObject *)__pyx_n_s__PG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_278));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_260));
- /* "pysam/csamtools.pyx":367
+ /* "csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<<
*
*
*/
- __pyx_k_tuple_279 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_279)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_279);
+ __pyx_k_tuple_261 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_261)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_261));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PN));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 0, ((PyObject *)__pyx_n_s__PN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 0, ((PyObject *)__pyx_n_s__PN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 1, ((PyObject *)__pyx_n_s__ID));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 1, ((PyObject *)__pyx_n_s__ID));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
__Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 2, ((PyObject *)__pyx_n_s__VN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 2, ((PyObject *)__pyx_n_s__VN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CL));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 3, ((PyObject *)__pyx_n_s__CL));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 3, ((PyObject *)__pyx_n_s__CL));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CL));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PP));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 4, ((PyObject *)__pyx_n_s__PP));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 4, ((PyObject *)__pyx_n_s__PP));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PP));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_279));
-
- /* "pysam/csamtools.pyx":3092
- * class Outs:
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1): # <<<<<<<<<<<<<<
- * self.streams = []
- * self.id = id
- */
- __pyx_k_tuple_280 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_280)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_280);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_280, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__id));
- PyTuple_SET_ITEM(__pyx_k_tuple_280, 1, ((PyObject *)__pyx_n_s__id));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_280));
- __pyx_k_codeobj_281 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_280, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 3092, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_281)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_k_tuple_282 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_282)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_282);
- __Pyx_INCREF(((PyObject *)__pyx_int_1));
- PyTuple_SET_ITEM(__pyx_k_tuple_282, 0, ((PyObject *)__pyx_int_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_int_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_282));
-
- /* "pysam/csamtools.pyx":3096
- * self.id = id
- *
- * def setdevice(self, filename): # <<<<<<<<<<<<<<
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
- */
- __pyx_k_tuple_283 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_283)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_283);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_283, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_283, 1, ((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
- PyTuple_SET_ITEM(__pyx_k_tuple_283, 2, ((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_283));
- __pyx_k_codeobj_284 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_283, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setdevice, 3096, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_284)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":3101
- * self.setfd(fd)
- *
- * def setfile(self, filename): # <<<<<<<<<<<<<<
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
- */
- __pyx_k_tuple_285 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_285)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_285);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_285, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_285, 1, ((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
- PyTuple_SET_ITEM(__pyx_k_tuple_285, 2, ((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_285));
- __pyx_k_codeobj_286 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_285, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setfile, 3101, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_286)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":3106
- * self.setfd(fd)
- *
- * def setfd(self, fd): # <<<<<<<<<<<<<<
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
- */
- __pyx_k_tuple_287 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_287)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_287);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_287, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
- PyTuple_SET_ITEM(__pyx_k_tuple_287, 1, ((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ofd));
- PyTuple_SET_ITEM(__pyx_k_tuple_287, 2, ((PyObject *)__pyx_n_s__ofd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ofd));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_287));
- __pyx_k_codeobj_288 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_287, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setfd, 3106, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_288)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":3114
- * os.close(fd) # Close other unit (look out, caller.)
- *
- * def restore(self): # <<<<<<<<<<<<<<
- * '''restore previous output stream'''
- * if self.streams:
- */
- __pyx_k_tuple_289 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_289)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_289);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_289, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_289));
- __pyx_k_codeobj_290 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_289, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__restore, 3114, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_290)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":3125
- * del self.streams[-1]
- *
- * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
- * args = (),
- * catch_stdout = True ):
- */
- __pyx_k_tuple_292 = PyTuple_New(16); if (unlikely(!__pyx_k_tuple_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_292);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__method));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 0, ((PyObject *)__pyx_n_s__method));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__method));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__args));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 1, ((PyObject *)__pyx_n_s__args));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__args));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__catch_stdout));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 2, ((PyObject *)__pyx_n_s__catch_stdout));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__catch_stdout));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stderr_h));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 3, ((PyObject *)__pyx_n_s__stderr_h));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stderr_h));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stderr_f));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 4, ((PyObject *)__pyx_n_s__stderr_f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stderr_f));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_h));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 5, ((PyObject *)__pyx_n_s__stdout_h));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_h));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_f));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 6, ((PyObject *)__pyx_n_s__stdout_f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_f));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_save));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 7, ((PyObject *)__pyx_n_s__stdout_save));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_save));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__cargs));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 8, ((PyObject *)__pyx_n_s__cargs));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cargs));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 9, ((PyObject *)__pyx_n_s__i));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 10, ((PyObject *)__pyx_n_s__n));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__retval));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 11, ((PyObject *)__pyx_n_s__retval));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__retval));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__inf));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 12, ((PyObject *)__pyx_n_s__inf));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__inf));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__out_stdout));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 13, ((PyObject *)__pyx_n_s__out_stdout));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__out_stdout));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__out_stderr));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 14, ((PyObject *)__pyx_n_s__out_stderr));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__out_stderr));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__a));
- PyTuple_SET_ITEM(__pyx_k_tuple_292, 15, ((PyObject *)__pyx_n_s__a));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_292));
- __pyx_k_codeobj_293 = (PyObject*)__Pyx_PyCode_New(3, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_292, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s___samtools_dispatch, 3125, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_293)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_261));
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
Py_FatalError("failed to import 'refnanny' module");
}
#endif
- __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", 0);
+ __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)");
if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #ifdef __Pyx_CyFunction_USED
- if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- #ifdef __Pyx_FusedFunction_USED
- if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- #ifdef __Pyx_Generator_USED
- if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __pyx_binding_PyCFunctionType_USED
+ if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if PY_MAJOR_VERSION >= 3
- {
- PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!PyDict_GetItemString(modules, "pysam.csamtools")) {
- if (unlikely(PyDict_SetItemString(modules, "pysam.csamtools", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- }
- #endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
#endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_module_is_main_pysam__csamtools) {
+ if (__pyx_module_is_main_csamtools) {
if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
}
/*--- Builtin init code ---*/
/*--- 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 ---*/
- __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- __pyx_vtabptr_5pysam_9csamtools_Fastafile = &__pyx_vtable_5pysam_9csamtools_Fastafile;
- __pyx_vtable_5pysam_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_5pysam_9csamtools_9Fastafile__fetch;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_Fastafile = &__pyx_type_5pysam_9csamtools_Fastafile;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
+ __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
+ if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
+ if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_5pysam_9csamtools_11AlignedRead_4__str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__;
- }
- }
- #endif
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_AlignedRead = &__pyx_type_5pysam_9csamtools_AlignedRead;
- __pyx_vtabptr_5pysam_9csamtools_Samfile = &__pyx_vtable_5pysam_9csamtools_Samfile;
- __pyx_vtable_5pysam_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *))__pyx_f_5pysam_9csamtools_7Samfile__buildHeader;
- __pyx_vtable_5pysam_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_getCurrent;
- __pyx_vtable_5pysam_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_cnext;
- __pyx_vtable_5pysam_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_5pysam_9csamtools_7Samfile_write;
- __pyx_vtable_5pysam_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int))__pyx_f_5pysam_9csamtools_7Samfile__getrname;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__.doc = __pyx_doc_9csamtools_11AlignedRead_2__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
+ }
+ }
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
+ __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
+ __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
+ __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
+ __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
+ __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
+ __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
+ if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__.doc = __pyx_doc_5pysam_9csamtools_7Samfile_42__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_Samfile = &__pyx_type_5pysam_9csamtools_Samfile;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_PileupProxy = &__pyx_type_5pysam_9csamtools_PileupProxy;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_PileupRead = &__pyx_type_5pysam_9csamtools_PileupRead;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRow = &__pyx_type_5pysam_9csamtools_IteratorRow;
- __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion = &__pyx_vtable_5pysam_9csamtools_IteratorRowRegion;
- __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_getCurrent;
- __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_cnext;
- __pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_wrapperbase_9csamtools_7Samfile_21__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
+ __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
+ __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
+ __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowRegion = &__pyx_type_5pysam_9csamtools_IteratorRowRegion;
- __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll = &__pyx_vtable_5pysam_9csamtools_IteratorRowAll;
- __pyx_vtable_5pysam_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_getCurrent;
- __pyx_vtable_5pysam_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_cnext;
- __pyx_type_5pysam_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
+ __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
+ __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
+ __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__;
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
}
}
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowAll = &__pyx_type_5pysam_9csamtools_IteratorRowAll;
- __pyx_type_5pysam_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
+ __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
- }
- }
- #endif
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = &__pyx_type_5pysam_9csamtools_IteratorRowAllRefs;
- __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection = &__pyx_vtable_5pysam_9csamtools_IteratorRowSelection;
- __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_getCurrent;
- __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_cnext;
- __pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
+ }
+ }
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
+ __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
+ __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
+ __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowSelection = &__pyx_type_5pysam_9csamtools_IteratorRowSelection;
- __pyx_vtabptr_5pysam_9csamtools_IteratorColumn = &__pyx_vtable_5pysam_9csamtools_IteratorColumn;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_cnext;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_getSequence;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_setMask;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_5pysam_9csamtools_14IteratorColumn_setupIteratorData;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_reset;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorColumn = &__pyx_type_5pysam_9csamtools_IteratorColumn;
- __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion = &__pyx_vtable_5pysam_9csamtools_IteratorColumnRegion;
- __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
- __pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
+ __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
+ __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
+ __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
+ __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
+ __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
+ __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
+ __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
+ __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
+ __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = &__pyx_type_5pysam_9csamtools_IteratorColumnRegion;
- __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
- __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
- __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion;
+ __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs;
+ __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
+ __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__.doc = __pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IndexedReads = &__pyx_type_5pysam_9csamtools_IndexedReads;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_SNPCall = &__pyx_type_5pysam_9csamtools_SNPCall;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
+ __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs;
+ if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IndexedReads = &__pyx_type_9csamtools_IndexedReads;
+ if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
+ if (PyType_Ready(&__pyx_Generator_type) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools___pyx_Generator = &__pyx_Generator_type;
+ __pyx_type_9csamtools___pyx_scope_struct__genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator;
+ if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_9csamtools___pyx_scope_struct__genexpr;
+ __pyx_type_9csamtools___pyx_scope_struct_1_genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator;
+ if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_9csamtools___pyx_scope_struct_1_genexpr;
/*--- Type import code ---*/
- __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
- #if CYTHON_COMPILING_IN_PYPY
- sizeof(PyTypeObject),
- #else
- sizeof(PyHeapTypeObject),
- #endif
- 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "pysam/csamtools.pyx":4
+ /* "csamtools.pyx":4
* # cython: profile=True
* # adds doc-strings for sphinx
* import tempfile # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tempfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":5
+ /* "csamtools.pyx":5
* # adds doc-strings for sphinx
* import tempfile
* import os # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__os, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":6
+ /* "csamtools.pyx":6
* import tempfile
* import os
* import sys # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sys, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":7
+ /* "csamtools.pyx":7
* import os
* import sys
* import types # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__types, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":8
+ /* "csamtools.pyx":8
* import sys
* import types
* import itertools # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__itertools, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":9
+ /* "csamtools.pyx":9
* import types
* import itertools
* import struct # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__struct, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":10
+ /* "csamtools.pyx":10
* import itertools
* import struct
* import ctypes # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__ctypes, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":11
+ /* "csamtools.pyx":11
* import struct
* import ctypes
* import collections # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__collections, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":12
+ /* "csamtools.pyx":12
* import ctypes
* import collections
* import re # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__re, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":13
+ /* "csamtools.pyx":13
* import collections
* import re
* import platform # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__platform, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":14
+ /* "csamtools.pyx":14
* import re
* import platform
* import warnings # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__warnings, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":23
+ /* "csamtools.pyx":23
* ## Python 3 compatibility functions
* ########################################################################
* IS_PYTHON3 = PY_MAJOR_VERSION >= 3 # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__IS_PYTHON3, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":32
+ /* "csamtools.pyx":32
* # filename encoding (copied from lxml.etree.pyx)
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding() # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
- __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":33
+ /* "csamtools.pyx":33
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding()
* if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None:
*/
- __pyx_t_3 = (__pyx_v_5pysam_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
+ __pyx_t_3 = (__pyx_v_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":34
+ /* "csamtools.pyx":34
* _FILENAME_ENCODING = sys.getfilesystemencoding()
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = sys.getdefaultencoding() # <<<<<<<<<<<<<<
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
- __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L2;
}
__pyx_L2:;
- /* "pysam/csamtools.pyx":35
+ /* "csamtools.pyx":35
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
* _FILENAME_ENCODING = 'ascii'
*
*/
- __pyx_t_3 = (__pyx_v_5pysam_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
+ __pyx_t_3 = (__pyx_v_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":36
+ /* "csamtools.pyx":36
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = 'ascii' # <<<<<<<<<<<<<<
* #cdef char* _C_FILENAME_ENCODING
*/
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = __pyx_n_s__ascii;
+ __pyx_v_9csamtools__FILENAME_ENCODING = __pyx_n_s__ascii;
goto __pyx_L3;
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":138
+ /* "csamtools.pyx":138
* DEF BAM_CDIFF = 8
*
* cdef char* CODE2CIGAR= "MIDNSHP=X" # <<<<<<<<<<<<<<
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
*/
- __pyx_v_5pysam_9csamtools_CODE2CIGAR = __pyx_k_250;
+ __pyx_v_9csamtools_CODE2CIGAR = __pyx_k_250;
- /* "pysam/csamtools.pyx":139
+ /* "csamtools.pyx":139
*
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3: # <<<<<<<<<<<<<<
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":140
+ /* "csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
- __pyx_t_1 = __pyx_pf_5pysam_9csamtools_2genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_9csamtools_1genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
}
/*else*/ {
- /* "pysam/csamtools.pyx":142
+ /* "csamtools.pyx":142
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
* CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
*
*/
- __pyx_t_1 = __pyx_pf_5pysam_9csamtools_5genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_9csamtools_3genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
}
__pyx_L4:;
- /* "pysam/csamtools.pyx":143
+ /* "csamtools.pyx":143
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
* CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) # <<<<<<<<<<<<<<
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CIGAR_REGEX, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":147
+ /* "csamtools.pyx":147
* #####################################################################
* ## set pysam stderr to /dev/null
* pysam_unset_stderr() # <<<<<<<<<<<<<<
*/
pysam_unset_stderr();
- /* "pysam/csamtools.pyx":151
+ /* "csamtools.pyx":151
* #####################################################################
* # hard-coded constants
* cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN" # <<<<<<<<<<<<<<
* cdef int max_pos = 2 << 29
*
*/
- __pyx_v_5pysam_9csamtools_bam_nt16_rev_table = __pyx_k_253;
+ __pyx_v_9csamtools_bam_nt16_rev_table = __pyx_k_253;
- /* "pysam/csamtools.pyx":152
+ /* "csamtools.pyx":152
* # hard-coded constants
* cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN"
* cdef int max_pos = 2 << 29 # <<<<<<<<<<<<<<
*
* #####################################################################
*/
- __pyx_v_5pysam_9csamtools_max_pos = 1073741824;
+ __pyx_v_9csamtools_max_pos = 1073741824;
- /* "pysam/csamtools.pyx":247
+ /* "csamtools.pyx":247
* (<object>f)(a)
*
* class PileupColumn(object): # <<<<<<<<<<<<<<
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "pysam/csamtools.pyx":260
+ /* "csamtools.pyx":260
* list of reads (:class:`pysam.PileupRead`) aligned to this column
* '''
* def __str__(self): # <<<<<<<<<<<<<<
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_12PileupColumn_1__str__, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_255)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_12PileupColumn___str__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____str__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":247
+ /* "csamtools.pyx":247
* (<object>f)(a)
*
* class PileupColumn(object): # <<<<<<<<<<<<<<
* all the reads that map to a certain target base.
*/
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_builtin_object);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_object);
__Pyx_GIVEREF(__pyx_builtin_object);
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_258)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s_257); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_254)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PileupColumn, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":304
+ /* "csamtools.pyx":304
* return 0
*
* class StderrStore(): # <<<<<<<<<<<<<<
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "pysam/csamtools.pyx":308
+ /* "csamtools.pyx":308
* stderr is captured.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
* return
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_1__init__, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_260)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":314
+ /* "csamtools.pyx":314
* self.stderr_save.setfd( self.stderr_h )
*
* def readAndRelease( self ): # <<<<<<<<<<<<<<
* return []
* self.stderr_save.restore()
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_3readAndRelease, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_262)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":323
+ /* "csamtools.pyx":323
* return lines
*
* def release(self): # <<<<<<<<<<<<<<
* return
* self.stderr_save.restore()
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_5release, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_264)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":329
+ /* "csamtools.pyx":329
* os.remove( self.stderr_f )
*
* def __del__(self): # <<<<<<<<<<<<<<
* self.release()
*
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_7__del__, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_266)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3__del__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____del__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":304
+ /* "csamtools.pyx":304
* return 0
*
* class StderrStore(): # <<<<<<<<<<<<<<
* '''
* stderr is captured.
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_267)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s_257); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_255)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":332
+ /* "csamtools.pyx":332
* self.release()
*
* class StderrStoreWindows(): # <<<<<<<<<<<<<<
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "pysam/csamtools.pyx":334
+ /* "csamtools.pyx":334
* class StderrStoreWindows():
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass # <<<<<<<<<<<<<<
* def readAndRelease(self): return []
* def release(self): pass
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_1__init__, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_269)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":335
+ /* "csamtools.pyx":335
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
* def readAndRelease(self): return [] # <<<<<<<<<<<<<<
* def release(self): pass
*
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_271)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":336
+ /* "csamtools.pyx":336
* def __init__(self): pass
* def readAndRelease(self): return []
* def release(self): pass # <<<<<<<<<<<<<<
*
* if platform.system()=='Windows':
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_5release, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_273)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":332
+ /* "csamtools.pyx":332
* self.release()
*
* class StderrStoreWindows(): # <<<<<<<<<<<<<<
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_274)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s_257); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_256)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStoreWindows, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":338
+ /* "csamtools.pyx":338
* def release(self): pass
*
* if platform.system()=='Windows': # <<<<<<<<<<<<<<
__pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Windows), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Windows), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":339
+ /* "csamtools.pyx":339
*
* if platform.system()=='Windows':
* del StderrStore # <<<<<<<<<<<<<<
*/
if (__Pyx_DelAttrString(__pyx_m, "StderrStore") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":340
+ /* "csamtools.pyx":340
* if platform.system()=='Windows':
* del StderrStore
* StderrStore = StderrStoreWindows # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStoreWindows); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStoreWindows); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L5;
}
__pyx_L5:;
- /* "pysam/csamtools.pyx":347
+ /* "csamtools.pyx":347
* ######################################################################
* # valid types for sam headers
* VALID_HEADER_TYPES = { "HD" : dict, # <<<<<<<<<<<<<<
* "SQ" : list,
* "RG" : list,
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)(&PyDict_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)(&PyDict_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":348
+ /* "csamtools.pyx":348
* # valid types for sam headers
* VALID_HEADER_TYPES = { "HD" : dict,
* "SQ" : list, # <<<<<<<<<<<<<<
* "RG" : list,
* "PG" : list,
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":349
+ /* "csamtools.pyx":349
* VALID_HEADER_TYPES = { "HD" : dict,
* "SQ" : list,
* "RG" : list, # <<<<<<<<<<<<<<
* "PG" : list,
* "CO" : list }
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":350
+ /* "csamtools.pyx":350
* "SQ" : list,
* "RG" : list,
* "PG" : list, # <<<<<<<<<<<<<<
* "CO" : list }
*
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":351
+ /* "csamtools.pyx":351
* "RG" : list,
* "PG" : list,
* "CO" : list } # <<<<<<<<<<<<<<
*
* # order of records within sam headers
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":354
+ /* "csamtools.pyx":354
*
* # order of records within sam headers
* VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<<
*
* # type conversions within sam header records
*/
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_275)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_257)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":357
+ /* "csamtools.pyx":357
*
* # type conversions within sam header records
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, # <<<<<<<<<<<<<<
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":358
+ /* "csamtools.pyx":358
* # type conversions within sam header records
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, # <<<<<<<<<<<<<<
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)(&PyInt_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)(&PyInt_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":359
+ /* "csamtools.pyx":359
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, # <<<<<<<<<<<<<<
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
* "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/csamtools.pyx":360
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":360
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, # <<<<<<<<<<<<<<
* "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
*
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":361
+ /* "csamtools.pyx":361
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
* "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } # <<<<<<<<<<<<<<
*
* # output order of fields within records
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":364
+ /* "csamtools.pyx":364
*
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_276)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_258)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":365
+ /* "csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_277)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_259)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":366
+ /* "csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<<
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_278)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_260)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":367
+ /* "csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<<
*
*
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_279)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_261)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":619
+ /* "csamtools.pyx":619
* header = None,
* port = None,
* add_sq_text = True, # <<<<<<<<<<<<<<
* check_header = True,
* check_sq = True,
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_k_21 = __pyx_t_4;
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_21 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":620
+ /* "csamtools.pyx":620
* port = None,
* add_sq_text = True,
* check_header = True, # <<<<<<<<<<<<<<
* check_sq = True,
* ):
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_k_22 = __pyx_t_4;
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_22 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":621
+ /* "csamtools.pyx":621
* add_sq_text = True,
* check_header = True,
* check_sq = True, # <<<<<<<<<<<<<<
* ):
* '''open a sam/bam file.
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_k_23 = __pyx_t_4;
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_23 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":900
+ /* "csamtools.pyx":900
* region = None,
* callback = None,
* until_eof = False ): # <<<<<<<<<<<<<<
* '''
* fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_k_54 = __pyx_t_4;
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_54 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1020
+ /* "csamtools.pyx":1020
* end = None,
* region = None,
* until_eof = False ): # <<<<<<<<<<<<<<
* '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
*
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_k_73 = __pyx_t_4;
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_73 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1937
+ /* "csamtools.pyx":1937
* int tid = 0,
* int start = 0,
* int end = max_pos, # <<<<<<<<<<<<<<
* int truncate = False,
* **kwargs ):
*/
- __pyx_k_128 = __pyx_v_5pysam_9csamtools_max_pos;
+ __pyx_k_128 = __pyx_v_9csamtools_max_pos;
- /* "pysam/csamtools.pyx":3090
+ /* "csamtools.pyx":3090
* return self._level
*
* class Outs: # <<<<<<<<<<<<<<
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "pysam/csamtools.pyx":3092
+ /* "csamtools.pyx":3092
* class Outs:
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1): # <<<<<<<<<<<<<<
* self.streams = []
* self.id = id
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_1__init__, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_281)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_282));
- if (PyObject_SetItem(__pyx_t_4, __pyx_n_s____init__, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3096
+ /* "csamtools.pyx":3096
* self.id = id
*
* def setdevice(self, filename): # <<<<<<<<<<<<<<
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_3setdevice, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_284)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__setdevice, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_1setdevice, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setdevice, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3101
+ /* "csamtools.pyx":3101
* self.setfd(fd)
*
* def setfile(self, filename): # <<<<<<<<<<<<<<
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_5setfile, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_286)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__setfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_2setfile, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfile, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3106
+ /* "csamtools.pyx":3106
* self.setfd(fd)
*
* def setfd(self, fd): # <<<<<<<<<<<<<<
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_7setfd, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_288)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__setfd, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_3setfd, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfd, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3114
+ /* "csamtools.pyx":3114
* os.close(fd) # Close other unit (look out, caller.)
*
* def restore(self): # <<<<<<<<<<<<<<
* '''restore previous output stream'''
* if self.streams:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_9restore, 0, NULL, __pyx_n_s_257, ((PyObject *)__pyx_k_codeobj_290)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__restore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_4restore, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__restore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3090
+ /* "csamtools.pyx":3090
* return self._level
*
* class Outs: # <<<<<<<<<<<<<<
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_4), "__doc__", ((PyObject *)__pyx_kp_s_291)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_4), __pyx_n_s__Outs, __pyx_n_s_257); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_262)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__Outs, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3127
+ /* "csamtools.pyx":3127
* def _samtools_dispatch( method,
* args = (),
* catch_stdout = True ): # <<<<<<<<<<<<<<
* '''call ``method`` in samtools providing arguments in args.
*
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_k_176 = __pyx_t_4;
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_k_176 = __pyx_t_1;
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3125
+ /* "csamtools.pyx":3125
* del self.streams[-1]
*
* def _samtools_dispatch( method, # <<<<<<<<<<<<<<
* args = (),
* catch_stdout = True ):
*/
- __pyx_t_4 = PyCFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s_257); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools__samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3836
+ /* "csamtools.pyx":3836
* if self.owns_samfile: samclose( self.fp )
*
* __all__ = ["Samfile", # <<<<<<<<<<<<<<
* "Fastafile",
* "IteratorRow",
*/
- __pyx_t_4 = PyList_New(9); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile));
- PyList_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_n_s__Samfile));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Samfile));
__Pyx_INCREF(((PyObject *)__pyx_n_s__Fastafile));
- PyList_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__Fastafile));
+ PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__Fastafile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Fastafile));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorRow));
- PyList_SET_ITEM(__pyx_t_4, 2, ((PyObject *)__pyx_n_s__IteratorRow));
+ PyList_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__IteratorRow));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorRow));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorColumn));
- PyList_SET_ITEM(__pyx_t_4, 3, ((PyObject *)__pyx_n_s__IteratorColumn));
+ PyList_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__IteratorColumn));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorColumn));
__Pyx_INCREF(((PyObject *)__pyx_n_s__AlignedRead));
- PyList_SET_ITEM(__pyx_t_4, 4, ((PyObject *)__pyx_n_s__AlignedRead));
+ PyList_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__AlignedRead));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__AlignedRead));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PileupColumn));
- PyList_SET_ITEM(__pyx_t_4, 5, ((PyObject *)__pyx_n_s__PileupColumn));
+ PyList_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__PileupColumn));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupColumn));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PileupProxy));
- PyList_SET_ITEM(__pyx_t_4, 6, ((PyObject *)__pyx_n_s__PileupProxy));
+ PyList_SET_ITEM(__pyx_t_1, 6, ((PyObject *)__pyx_n_s__PileupProxy));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupProxy));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PileupRead));
- PyList_SET_ITEM(__pyx_t_4, 7, ((PyObject *)__pyx_n_s__PileupRead));
+ PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__PileupRead));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupRead));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IndexedReads));
- PyList_SET_ITEM(__pyx_t_4, 8, ((PyObject *)__pyx_n_s__IndexedReads));
+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__IndexedReads));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndexedReads));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1
+ /* "csamtools.pyx":1
* # cython: embedsignature=True # <<<<<<<<<<<<<<
* # cython: profile=True
* # adds doc-strings for sphinx
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ 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;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_4);
if (__pyx_m) {
- __Pyx_AddTraceback("init pysam.csamtools", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init csamtools", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init pysam.csamtools");
+ PyErr_SetString(PyExc_ImportError, "init csamtools");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
}
/* Runtime support code */
+
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
return result;
}
+
#if CYTHON_PROFILE
+
static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
PyFrameObject** frame,
const char *funcname,
}
return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
}
+
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
PyCodeObject *py_code = 0;
+
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
py_srcfile = PyString_FromString(srcfile);
py_srcfile = PyUnicode_FromString(srcfile);
#endif
if (!py_funcname | !py_srcfile) goto bad;
+
py_code = PyCode_New(
0, /*int argcount,*/
#if PY_MAJOR_VERSION >= 3
firstlineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
+
bad:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
+
return py_code;
}
-#endif /* CYTHON_PROFILE */
-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
- Py_ssize_t length;
- if (unlikely((start < 0) | (stop < 0))) {
- length = strlen(cstring);
- if (start < 0) {
- start += length;
- if (start < 0)
- start = 0;
- }
- if (stop < 0)
- stop += length;
- }
- length = stop - start;
- if (unlikely(length <= 0))
- return PyUnicode_FromUnicode(NULL, 0);
- cstring += start;
- if (decode_func) {
- return decode_func(cstring, length, errors);
- } else {
- return PyUnicode_Decode(cstring, length, encoding, errors);
- }
-}
+#endif /* CYTHON_PROFILE */
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
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;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
}
+
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
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;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
}
+
#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ /* cause is unused */
Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
+ 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 (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
}
#if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
+ if (!PyClass_Check(type))
#else
- if (PyType_Check(type)) {
+ if (!PyType_Check(type))
#endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
+ {
+ /* 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)) {
}
#endif
}
+
__Pyx_ErrRestore(type, value, tb);
return;
raise_error:
Py_XDECREF(tb);
return;
}
+
#else /* Python 3+ */
+
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
}
if (value == Py_None)
value = 0;
+
if (PyExceptionInstance_Check(type)) {
if (value) {
PyErr_SetString(PyExc_TypeError,
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
+ } else if (!PyExceptionClass_Check(type)) {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause && cause != Py_None) {
+
+ if (cause) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
"BaseException");
goto bad;
}
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
PyException_SetCause(value, fixed_cause);
}
+
PyErr_SetObject(type, value);
+
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
Py_XDECREF(tmp_tb);
}
}
+
bad:
- Py_XDECREF(owned_instance);
return;
}
#endif
{
PyObject* key = 0;
Py_ssize_t pos = 0;
-#if CPYTHON_COMPILING_IN_PYPY
- if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
- goto invalid_keyword;
- return 1;
-#else
while (PyDict_Next(kwdict, &pos, &key, 0)) {
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
#endif
- if (unlikely(!PyUnicode_Check(key)))
- goto invalid_keyword_type;
+ goto invalid_keyword_type;
}
if ((!kw_allowed) && unlikely(key))
goto invalid_keyword;
PyErr_Format(PyExc_TypeError,
"%s() keywords must be strings", function_name);
return 0;
-#endif
invalid_keyword:
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_AsString(kw_name));
+ PyString_AS_STRING(kw_name));
#endif
}
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
+
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
}
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
+ if (*name) {
values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
+ } else {
+ /* unexpected keyword found */
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
}
}
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
{
Py_ssize_t num_expected;
const char *more_or_less;
+
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
*type = local_type;
*value = local_value;
*tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
+ 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_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
+ these objects (XDECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
return 0;
bad:
*type = 0;
return -1;
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+}
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ } else if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
PyErr_Clear();
return 0;
}
}
return 0;
-#endif
}
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
}
static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
}
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_base && type->tp_base->tp_traverse)
- return type->tp_base->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_base && type->tp_base->tp_clear)
- type->tp_base->tp_clear(obj);
-}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
}
+
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
goto bad;
#if PY_VERSION_HEX >= 0x02050000
{
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- }
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
}
#else
if (level>0) {
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);
PyObject *modname) {
PyObject *result;
PyObject *metaclass;
+
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
+
+ /* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
return result;
}
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- }
- if (op->func_doc == 0) {
- Py_INCREF(Py_None);
- return Py_None;
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- op->func_doc = Py_None; /* Mark as deleted */
- else
- op->func_doc = value;
- Py_INCREF(op->func_doc);
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (op->func_name == NULL) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (value == NULL || !PyUnicode_Check(value)) {
-#else
- if (value == NULL || !PyString_Check(value)) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (op->func_dict == NULL) {
- op->func_dict = PyDict_New();
- if (op->func_dict == NULL)
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (value == NULL) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (!PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- PyObject* dict = PyModule_GetDict(__pyx_m);
- Py_XINCREF(dict);
- return dict;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
-{
- if (op->defaults_tuple) {
- Py_INCREF(op->defaults_tuple);
- return op->defaults_tuple;
- }
- if (op->defaults_getter) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (res) {
- Py_INCREF(res);
- op->defaults_tuple = res;
- }
- return res;
- }
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
- PyObject *closure, PyObject *module, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
+
+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->flags = flags;
- op->func_weakreflist = NULL;
op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
+ Py_XINCREF(self);
+ op->func.m_self = self;
Py_XINCREF(module);
op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_getter = NULL;
PyObject_GC_Track(op);
- return (PyObject *) op;
+ return (PyObject *)op;
}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
-}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
+
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
PyObject_GC_Del(m);
}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
+
+static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
if (obj == Py_None)
- obj = NULL;
+ obj = NULL;
return PyMethod_New(func, obj, type);
}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
- PyObject *func_name = __Pyx_CyFunction_get_name(op);
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- func_name, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(func_name), (void *)op);
-#endif
-}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
- if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+
+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_CyFunctionType = &__pyx_CyFunctionType_type;
+ }
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
return 0;
-}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, sizeof(size));
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
+
}
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint64_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint64_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint64_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint64_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
- #else
- uint64_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyBytes_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+ else
+ return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+ } else {
+ int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
}
- #endif
- return (uint64_t)-1;
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
}
}
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint32_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint32_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint32_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint32_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
- #else
- uint32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
+ return (equals == Py_EQ);
+ } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
+ if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]);
+ else
+ return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]);
+ } else {
+ int result = PyUnicode_Compare(s1, s2);
+ if ((result == -1) && unlikely(PyErr_Occurred()))
+ return -1;
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
}
- #endif
- return (uint32_t)-1;
+ } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
}
}
}
}
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint32_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint32_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint32_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint32_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint32_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint32_t)-1;
+ }
+}
+
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
const int is_unsigned = const_zero < neg_one;
}
}
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
+ const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint64_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint64_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint64_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint64_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint64_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint64_t)-1;
+ }
+}
+
static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
const int is_unsigned = const_zero < neg_one;
else
return (uint8_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
- #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
- #else
uint8_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
if (likely(!ret))
return val;
}
- #endif
return (uint8_t)-1;
}
}
else
return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
- #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
- #else
int32_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
if (likely(!ret))
return val;
}
- #endif
return (int32_t)-1;
}
}
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
+
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
+
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
+
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
}
-static PyObject *__Pyx_Generator_Next(PyObject *self);
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
-static PyObject *__Pyx_Generator_Close(PyObject *self);
-static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static PyTypeObject *__pyx_GeneratorType = 0;
-#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
-#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
- PyObject *et, *ev, *tb;
- PyObject *value = NULL;
- __Pyx_ErrFetch(&et, &ev, &tb);
- if (!et) {
- Py_XDECREF(tb);
- Py_XDECREF(ev);
- Py_INCREF(Py_None);
- *pvalue = Py_None;
- return 0;
- }
- if (unlikely(et != PyExc_StopIteration) &&
- unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- if (likely(et == PyExc_StopIteration)) {
- if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
- if (!ev) {
- Py_INCREF(Py_None);
- ev = Py_None;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
- *pvalue = ev;
- return 0;
- }
- }
- PyErr_NormalizeException(&et, &ev, &tb);
- if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
-#if PY_VERSION_HEX >= 0x030300A0
- value = ((PyStopIterationObject *)ev)->value;
- Py_INCREF(value);
- Py_DECREF(ev);
-#else
- {
- PyObject* args = PyObject_GetAttrString(ev, "args");
- Py_DECREF(ev);
- if (likely(args)) {
- value = PyObject_GetItem(args, 0);
- Py_DECREF(args);
- }
- if (unlikely(!value)) {
- __Pyx_ErrRestore(NULL, NULL, NULL);
- Py_INCREF(Py_None);
- value = Py_None;
- }
- }
-#endif
- *pvalue = value;
- return 0;
-}
-#endif
-static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
- PyObject *exc_type = self->exc_type;
- PyObject *exc_value = self->exc_value;
- PyObject *exc_traceback = self->exc_traceback;
+static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self)
+{
+ Py_XDECREF(self->exc_type);
+ Py_XDECREF(self->exc_value);
+ Py_XDECREF(self->exc_traceback);
+
self->exc_type = NULL;
self->exc_value = NULL;
self->exc_traceback = NULL;
- Py_XDECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_traceback);
}
-static CYTHON_INLINE
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
- if (unlikely(gen->is_running)) {
+
+static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value)
+{
+ PyObject *retval;
+
+ if (self->is_running) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return 1;
+ return NULL;
}
- return 0;
-}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
- PyObject *retval;
- assert(!self->is_running);
- if (unlikely(self->resume_label == 0)) {
- if (unlikely(value && value != Py_None)) {
+
+ if (self->resume_label == 0) {
+ if (value && value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"can't send non-None value to a "
"just-started generator");
return NULL;
}
}
- if (unlikely(self->resume_label == -1)) {
+
+ if (self->resume_label == -1) {
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
- if (value) {
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Generators always return to their most recent caller, not
- * necessarily their creator. */
- if (self->exc_traceback) {
- PyThreadState *tstate = PyThreadState_GET();
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_XINCREF(tstate->frame);
- assert(f->f_back == NULL);
- f->f_back = tstate->frame;
- }
-#endif
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
- &self->exc_traceback);
- } else {
+
+
+ if (value)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
__Pyx_Generator_ExceptionClear(self);
- }
+
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
- if (retval) {
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
- &self->exc_traceback);
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Don't keep the reference to f_back any longer than necessary. It
- * may keep a chain of frames alive or it could create a reference
- * cycle. */
- if (self->exc_traceback) {
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_CLEAR(f->f_back);
- }
-#endif
- } else {
+
+ if (retval)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
__Pyx_Generator_ExceptionClear(self);
- }
+
return retval;
}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
- PyObject *ret;
- PyObject *val = NULL;
- __Pyx_Generator_Undelegate(gen);
- __Pyx_PyGen_FetchStopIterationValue(&val);
- ret = __Pyx_Generator_SendEx(gen, val);
- Py_XDECREF(val);
- return ret;
-}
-static PyObject *__Pyx_Generator_Next(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- ret = Py_TYPE(yf)->tp_iternext(yf);
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, Py_None);
-}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Send(yf, value);
- } else {
- if (value == Py_None)
- ret = PyIter_Next(yf);
- else
- ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
- }
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, value);
+
+static PyObject *__Pyx_Generator_Next(PyObject *self)
+{
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None);
}
-static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
- PyObject *retval = NULL;
- int err = 0;
- if (__Pyx_Generator_CheckExact(yf)) {
- retval = __Pyx_Generator_Close(yf);
- if (!retval)
- return -1;
- } else {
- PyObject *meth;
- gen->is_running = 1;
- meth = PyObject_GetAttrString(yf, "close");
- if (unlikely(!meth)) {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_WriteUnraisable(yf);
- }
- PyErr_Clear();
- } else {
- retval = PyObject_CallFunction(meth, NULL);
- Py_DECREF(meth);
- if (!retval)
- err = -1;
- }
- gen->is_running = 0;
- }
- Py_XDECREF(retval);
- return err;
+
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
+{
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value);
}
-static PyObject *__Pyx_Generator_Close(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject *retval, *raised_exception;
- PyObject *yf = gen->yieldfrom;
- int err = 0;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- Py_INCREF(yf);
- err = __Pyx_Generator_CloseIter(gen, yf);
- __Pyx_Generator_Undelegate(gen);
- Py_DECREF(yf);
- }
- if (err == 0)
+
+static PyObject *__Pyx_Generator_Close(PyObject *self)
+{
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
+ PyObject *retval;
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(gen, NULL);
+ retval = __Pyx_Generator_SendEx(generator, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
- raised_exception = PyErr_Occurred();
- if (!raised_exception
- || raised_exception == PyExc_StopIteration
-#if PY_VERSION_HEX >= 0x02050000
- || raised_exception == PyExc_GeneratorExit
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
+#if PY_VERSION_HEX < 0x02050000
+ if (PyErr_ExceptionMatches(PyExc_StopIteration))
+#else
+ if (PyErr_ExceptionMatches(PyExc_StopIteration)
+ || PyErr_ExceptionMatches(PyExc_GeneratorExit))
#endif
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- if (raised_exception) PyErr_Clear(); /* ignore these errors */
+ PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds)
+{
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
- PyObject *yf = gen->yieldfrom;
+
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- Py_INCREF(yf);
-#if PY_VERSION_HEX >= 0x02050000
- if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
- int err = __Pyx_Generator_CloseIter(gen, yf);
- Py_DECREF(yf);
- __Pyx_Generator_Undelegate(gen);
- if (err < 0)
- return __Pyx_Generator_SendEx(gen, NULL);
- goto throw_here;
- }
-#endif
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Throw(yf, args);
- } else {
- PyObject *meth = PyObject_GetAttrString(yf, "throw");
- if (unlikely(!meth)) {
- Py_DECREF(yf);
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- gen->is_running = 0;
- return NULL;
- }
- PyErr_Clear();
- __Pyx_Generator_Undelegate(gen);
- gen->is_running = 0;
- goto throw_here;
- }
- ret = PyObject_CallObject(meth, args);
- Py_DECREF(meth);
- }
- gen->is_running = 0;
- Py_DECREF(yf);
- if (!ret) {
- ret = __Pyx_Generator_FinishDelegation(gen);
- }
- return ret;
- }
-throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(gen, NULL);
-}
-static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_VISIT(gen->closure);
- Py_VISIT(gen->classobj);
- Py_VISIT(gen->yieldfrom);
- Py_VISIT(gen->exc_type);
- Py_VISIT(gen->exc_value);
- Py_VISIT(gen->exc_traceback);
- return 0;
-}
-static int __Pyx_Generator_clear(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->yieldfrom);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject_GC_UnTrack(gen);
- if (gen->gi_weakreflist != NULL)
- PyObject_ClearWeakRefs(self);
- PyObject_GC_Track(self);
- if (gen->resume_label > 0) {
- Py_TYPE(gen)->tp_del(self);
- if (self->ob_refcnt > 0)
- return; /* resurrected. :( */
- }
- PyObject_GC_UnTrack(self);
- __Pyx_Generator_clear(self);
- PyObject_GC_Del(gen);
-}
-static void __Pyx_Generator_del(PyObject *self) {
- PyObject *res;
- PyObject *error_type, *error_value, *error_traceback;
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- if (gen->resume_label <= 0)
- return ;
- assert(self->ob_refcnt == 0);
- self->ob_refcnt = 1;
- __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
- res = __Pyx_Generator_Close(self);
- if (res == NULL)
- PyErr_WriteUnraisable(self);
- else
- Py_DECREF(res);
- __Pyx_ErrRestore(error_type, error_value, error_traceback);
- /* Undo the temporary resurrection; can't use DECREF here, it would
- * cause a recursive call.
- */
- assert(self->ob_refcnt > 0);
- if (--self->ob_refcnt == 0)
- return; /* this is the normal path out */
- /* close() resurrected it! Make it look like the original Py_DECREF
- * never happened.
- */
- {
- Py_ssize_t refcnt = self->ob_refcnt;
- _Py_NewReference(self);
- self->ob_refcnt = refcnt;
- }
-#if CYTHON_COMPILING_FOR_CPYTHON
- assert(PyType_IS_GC(self->ob_type) &&
- _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
- /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
- * we need to undo that. */
- _Py_DEC_REFTOTAL;
-#endif
- /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
- * chain, so no more to do there.
- * If COUNT_ALLOCS, the original decref bumped tp_frees, and
- * _Py_NewReference bumped tp_allocs: both of those need to be
- * undone.
- */
-#ifdef COUNT_ALLOCS
- --Py_TYPE(self)->tp_frees;
- --Py_TYPE(self)->tp_allocs;
-#endif
-}
-static PyMemberDef __pyx_Generator_memberlist[] = {
- {(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
- T_BOOL,
-#else
- T_BYTE,
-#endif
- offsetof(__pyx_GeneratorObject, is_running),
- READONLY,
- NULL},
- {0, 0, 0, 0, 0}
-};
-static PyMethodDef __pyx_Generator_methods[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
- {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
- {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
- {0, 0, 0, 0}
-};
-static PyTypeObject __pyx_GeneratorType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("generator"), /*tp_name*/
- sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_Generator_methods, /*tp_methods*/
- __pyx_Generator_memberlist, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- __Pyx_Generator_del, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure) {
- __pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
- if (gen == NULL)
- return NULL;
- gen->body = body;
- gen->closure = closure;
- Py_XINCREF(closure);
- gen->is_running = 0;
- gen->resume_label = 0;
- gen->classobj = NULL;
- gen->yieldfrom = NULL;
- gen->exc_type = NULL;
- gen->exc_value = NULL;
- gen->exc_traceback = NULL;
- gen->gi_weakreflist = NULL;
- PyObject_GC_Track(gen);
- return gen;
-}
-static int __pyx_Generator_init(void) {
- __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
- __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
- if (PyType_Ready(&__pyx_GeneratorType_type)) {
- return -1;
- }
- __pyx_GeneratorType = &__pyx_GeneratorType_type;
- return 0;
+ return __Pyx_Generator_SendEx(generator, NULL);
}
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+ int lineno, const char *filename) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
return -1;
}
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
if (!py_name)
goto bad;
result = PyObject_GetAttr(py_module, py_name);
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+ if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
}
#endif
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
}
+#endif
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
+
+static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
+ int __pyx_lineno, const char *__pyx_filename) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
#if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
+ py_srcfile = PyString_FromString(__pyx_filename);
#else
- py_srcfile = PyUnicode_FromString(filename);
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
#endif
if (!py_srcfile) goto bad;
- if (c_line) {
+ if (__pyx_clineno) {
#if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#endif
}
else {
#endif
}
if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_code = PyCode_New(
0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
+ #endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
+ __pyx_lineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
+ if (!py_code) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
+ py_frame->f_lineno = __pyx_lineno;
PyTraceBack_Here(py_frame);
bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
return 0;
}
-
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
-/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */
+/* Generated by Cython 0.16 on Tue Jan 15 06:50:15 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
+
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
#define __fastcall
#endif
#endif
+
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
+
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
+
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
+
+#if CYTHON_COMPILING_IN_PYPY
+ #define __Pyx_PyCFunction_Call PyObject_Call
+#else
+ #define __Pyx_PyCFunction_Call PyCFunction_Call
+#endif
+
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
+ #define PyNumber_Index(o) PyNumber_Int(o)
+ #define PyIndex_Check(o) PyNumber_Check(o)
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
+
typedef struct {
void *buf;
PyObject *obj;
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
+
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
+
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
+
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
+
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
+
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+
+
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
#define PyBytes_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)
#ifndef PySet_CheckExact
#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_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
+
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#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)
(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
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) (n)
#endif
-
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
Py_INCREF(r);
return r;
}
- } else { /* inlined PySequence_GetItem() */
+ }
+ else if (likely(i >= 0)) {
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return NULL;
- i += l;
- }
return m->sq_item(o, i);
}
}
-#else
- if (PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
-#if CYTHON_COMPILING_IN_PYPY
-#define __Pyx_PyObject_AsDouble(obj) \
-(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
- likely(PyInt_CheckExact(obj)) ? \
- PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
-#else
#define __Pyx_PyObject_AsDouble(obj) \
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-#endif
static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
+ if (unlikely(d == Py_None)) {
+ __Pyx_RaiseNoneIndexingError();
+ return NULL;
+ }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
- int result = PySequence_Contains(seq, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
+}
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
+ return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
- int result = PyDict_Contains(dict, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len)) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
- }
- return PyList_Append(list, x);
-}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
-
static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (unlikely(PyList_Append(L, x) < 0)) return NULL;
+ if (PyList_Append(L, x) < 0) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- } else {
+ }
+ else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
}
}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
-static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2,
- int is_tuple, int has_known_size, int decref_tuple);
-
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
- Py_ssize_t* p_orig_length, int* p_is_dict);
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
- PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
-
#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_SetItemInt_Fast(o, i, v) : \
__Pyx_SetItemInt_Generic(o, to_py_func(i), v))
return r;
}
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
-#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
Py_DECREF(old);
return 1;
}
- } else { /* inlined PySequence_SetItem() */
+ }
+ else if (likely(i >= 0)) {
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_ass_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return -1;
- i += l;
- }
return m->sq_ass_item(o, i, v);
}
}
-#else
-#if CYTHON_COMPILING_IN_PYPY
- if (PySequence_Check(o) && !PyDict_Check(o)) {
-#else
- if (PySequence_Check(o)) {
-#endif
- return PySequence_SetItem(o, i, v);
- }
-#endif
return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
}
#endif /* PyAnySet_CheckExact (<= Py2.4) */
#endif /* < Py2.5 */
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
-
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 CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+#include <string.h>
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
+
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
#define __Pyx_Generator_USED
#include <structmember.h>
-#include <frameobject.h>
typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
typedef struct {
PyObject_HEAD
__pyx_generator_body_t body;
PyObject *closure;
+ int is_running;
+ int resume_label;
PyObject *exc_type;
PyObject *exc_value;
PyObject *exc_traceback;
PyObject *gi_weakreflist;
PyObject *classobj;
- PyObject *yieldfrom;
- int resume_label;
- char is_running; // using T_BOOL for property below requires char value
} __pyx_GeneratorObject;
static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject *closure);
static int __pyx_Generator_init(void);
-static int __Pyx_Generator_clear(PyObject* self);
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
-#else
-#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
-#endif
static int __Pyx_check_binary_version(void);
#endif
#endif
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
static char __pyx_k_126[] = "needs to be checked";
static char __pyx_k_128[] = "[|/\\\\]";
static char __pyx_k_130[] = "^[ACGTN]+$";
-static char __pyx_k_134[] = "/ifs/devel/pysam/pysam/cvcf.pyx";
+static char __pyx_k_134[] = "/home/andreas/devel/pysam/pysam/cvcf.pyx";
static char __pyx_k_135[] = "pysam.cvcf";
static char __pyx_k_138[] = "id numbertype number type description missingvalue";
static char __pyx_k_140[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_fa = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("get_sequence (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
PyObject* values[4] = {0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* if not fa: return "N"*(end-start)
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
* sequence = fa.fetch(chrom, start, end).upper()
* if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_3) {
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_regions (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_2parse_regions(__pyx_self, ((PyObject *)__pyx_v_string));
__Pyx_RefNannyFinishContext();
return __pyx_r;
for (;;) {
if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
} else {
__pyx_t_2 = __pyx_t_4(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_vcf = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_vcf = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_error = 0;
PyObject *__pyx_v_opt = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("error (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject* values[3] = {0,0,0};
/* "pysam/cvcf.pyx":121
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* else: alt = alt.upper().split(',')
* return alt
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = __Pyx_PyString_Equals(__pyx_v_alt, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_2) {
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
* else:
* try: qual = float(qual)
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, ((PyObject *)__pyx_kp_b_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = __Pyx_PyBytes_Equals(__pyx_v_qual, ((PyObject *)__pyx_kp_b_9), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_2) {
__Pyx_INCREF(__pyx_int_neg_1);
__Pyx_DECREF(__pyx_v_qual);
*/
__pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!__pyx_t_3) {
__pyx_t_2 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_n_b__PASS), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_n_b__PASS), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_4) {
__pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b__0), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b__0), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
*/
__pyx_t_1 = PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
for (;;) {
if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else {
__pyx_t_8 = __pyx_t_10(__pyx_t_9);
if (unlikely(!__pyx_t_8)) {
__pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
* else: value = ",".join(["."]*expected)
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
* self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_5) {
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_13 = PyObject_RichCompare(__pyx_t_8, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_13); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_RichCompare(__pyx_t_8, __pyx_v_expected, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_vcffile = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcffile,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcffile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcffile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcffile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_buffer;
int __pyx_v_len;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_v_regions = 0;
PyObject *__pyx_v_lines = 0;
PyObject *__pyx_v_leftalign = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s___copy,&__pyx_n_s__reference,&__pyx_n_s__regions,&__pyx_n_s__lines,&__pyx_n_s__leftalign,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s___copy,&__pyx_n_s__reference,&__pyx_n_s__regions,&__pyx_n_s__lines,&__pyx_n_s__leftalign,0};
PyObject* values[6] = {0,0,0,0,0,0};
__pyx_defaults *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults, __pyx_self);
values[1] = ((PyObject *)((PyObject *)Py_None));
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
for (;;) {
if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
} else {
__pyx_t_1 = __pyx_t_4(__pyx_t_2);
if (unlikely(!__pyx_t_1)) {
* self._leftalign = _copy._leftalign
* self._header = _copy._header[:]
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_7) {
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_error = 0;
PyObject *__pyx_v_opt = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("error (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject* values[4] = {0,0,0,0};
/* "pysam/cvcf.pyx":335
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PySequence_Contains(__pyx_t_1, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_4 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_4 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_4);
- #else
- __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_5 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
index = 1; __pyx_t_4 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_4)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_4);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = NULL;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
goto __pyx_L5_unpacking_done;
__pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
}
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Warning));
__pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_4, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PySequence_Contains(__pyx_t_4, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_4 = __Pyx_GetItemInt_List(((PyObject *)__pyx_t_3), __pyx_t_2, sizeof(int), __Pyx_PyBool_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
*/
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_3, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PySequence_Contains(__pyx_t_3, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_format = 0;
PyObject *__pyx_v_filter = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__format,&__pyx_n_s__filter,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_format (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__format,&__pyx_n_s__filter,0};
PyObject* values[4] = {0,0,0,0};
__pyx_defaults1 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_self);
values[3] = __pyx_dynamic_args->__pyx_arg_filter;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_31), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_33), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_35), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
*/
__pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
*/
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_4) {
*/
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_9 = __pyx_t_3;
* # missing description
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_4 = (__Pyx_PyDict_Contains(((PyObject *)__pyx_n_s__descr), ((PyObject *)__pyx_v_data), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
/* "pysam/cvcf.pyx":381
*/
__pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!((int)__pyx_t_4)) {
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = ((int)__pyx_t_9);
} else {
__pyx_t_3 = ((int)__pyx_t_4);
}
if (!__pyx_t_3) {
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Character), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Character), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_9 = ((int)__pyx_t_4);
} else {
__pyx_t_9 = __pyx_t_3;
}
if (!__pyx_t_9) {
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__String), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__String), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = ((int)__pyx_t_3);
} else {
__pyx_t_4 = __pyx_t_9;
}
if (!__pyx_t_4) {
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = ((int)__pyx_t_9);
} else {
__pyx_t_3 = __pyx_t_4;
*/
__pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!((int)__pyx_t_4)) {
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_9 = ((int)__pyx_t_3);
} else {
__pyx_t_9 = ((int)__pyx_t_4);
*/
__pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_t = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L31;
}
* elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
* elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
*/
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_53), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_53), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
*/
__pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_54), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_54), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_t = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L31;
}
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
*/
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_55), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_55), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
*/
__pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_t = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L31;
}
* # abbreviations added in VCF version v4.1
* elif data['number'] == 'A': t = self.NT_ALLELES
*/
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_56), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
*/
__pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_n_s__A), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_t = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L31;
}
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__G), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_n_s__G), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
* self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
* # force type 'Flag' if no number
*/
- __pyx_t_10 = PyObject_RichCompare(__pyx_v_n, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_v_n, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_9) {
__pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Flag), Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Flag), Py_NE); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __pyx_t_4;
} else {
__pyx_t_3 = __pyx_t_9;
* # force type 'Flag' if no number
* data['type'] = 'Flag'
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_57); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_57); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "pysam/cvcf.pyx":412
* self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
* def format_format( self, fmt, filter=False ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
if (unlikely(!__pyx_v_t)) { __Pyx_RaiseUnboundLocalError("t"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_15 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing)); if (!__pyx_t_15) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_v_n);
PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_v_n);
__Pyx_GIVEREF(__pyx_v_n);
- PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_t_15);
__Pyx_GIVEREF(__pyx_t_15);
__pyx_t_5 = 0;
- __pyx_t_1 = 0;
+ __pyx_t_10 = 0;
__pyx_t_2 = 0;
__pyx_t_15 = 0;
- __pyx_t_15 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_r = __pyx_t_15;
__pyx_t_15 = 0;
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_fmt = 0;
PyObject *__pyx_v_filter = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fmt,&__pyx_n_s__filter,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("format_format (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fmt,&__pyx_n_s__filter,0};
PyObject* values[3] = {0,0,0};
__pyx_defaults2 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_self);
values[2] = __pyx_dynamic_args->__pyx_arg_filter;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fmt)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fmt);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_6 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_6); __pyx_t_8 = 0;
for (;;) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_6)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_6, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++;
if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_11 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_10 = PyList_GET_ITEM(sequence, 0);
__pyx_t_11 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_10);
__Pyx_INCREF(__pyx_t_11);
- #else
- __pyx_t_10 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
index = 1; __pyx_t_11 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_11)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_11);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
goto __pyx_L9_unpacking_done;
__pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_13 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_v);
__pyx_v_v = __pyx_t_11;
__pyx_t_11 = 0;
- if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_v_v))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_v_v))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_2); __pyx_t_8 = 0;
for (;;) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++;
if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_11 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_11 = PyList_GET_ITEM(sequence, 0);
__pyx_t_10 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_11);
__Pyx_INCREF(__pyx_t_10);
- #else
- __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
index = 1; __pyx_t_10 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_10)) goto __pyx_L12_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
goto __pyx_L13_unpacking_done;
__pyx_L12_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_13 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L13_unpacking_done:;
}
__pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- if (unlikely(__Pyx_PyList_Append(__pyx_t_6, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_6, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
PyObject *__pyx_v_format = 0;
PyObject *__pyx_v_formatdict = 0;
PyObject *__pyx_v_alt = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("get_expected (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0};
PyObject* values[4] = {0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
PyObject *__pyx_v_key = 0;
PyObject *__pyx_v_data = 0;
PyObject *__pyx_v_line = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__formatdict,&__pyx_n_s__key,&__pyx_n_s__data,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_add_definition (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__formatdict,&__pyx_n_s__key,&__pyx_n_s__data,&__pyx_n_s__line,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[4])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* self.error(line,self.ERROR_UNKNOWN_KEY,key)
* if data == None:
*/
- __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_v_formatdict, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PySequence_Contains(__pyx_v_formatdict, __pyx_v_key))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
* formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
* return
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_1) {
*/
__pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, ((PyObject *)__pyx_t_4), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, ((PyObject *)__pyx_t_4), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_t_4)), Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_t_4)), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
*/
__pyx_t_4 = __Pyx_GetItemInt(__pyx_v_data, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_4)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_4)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
PyObject *__pyx_v_key = 0;
PyObject *__pyx_v_value = 0;
PyObject *__pyx_v_separator = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__data,&__pyx_n_s__format,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__separator,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("format_formatdata (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__data,&__pyx_n_s__format,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__separator,0};
PyObject* values[6] = {0,0,0,0,0,0};
__pyx_defaults3 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_self);
values[3] = __pyx_dynamic_args->__pyx_arg_key;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(((PyObject *)__pyx_t_2))), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(((PyObject *)__pyx_t_2))), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
for (;;) {
if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++;
} else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++;
} else {
__pyx_t_7 = __pyx_t_9(__pyx_t_2);
if (unlikely(!__pyx_t_7)) {
__pyx_t_10 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, __pyx_t_10, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, __pyx_t_10, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++;
} else {
__pyx_t_6 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_6)) {
* sdata.sort()
* if 'GT' in data:
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_k, ((PyObject *)__pyx_n_s__GT), Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_k, ((PyObject *)__pyx_n_s__GT), Py_NE); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
__pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
* sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
* for k,v in sdata:
*/
- __pyx_t_3 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__GT), __pyx_v_data, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PySequence_Contains(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":480
__pyx_t_6 = ((PyObject *)__pyx_v_sdata); __Pyx_INCREF(__pyx_t_6); __pyx_t_4 = 0;
for (;;) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_6)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_6, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_7 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_7);
- #else
- __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_10 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
index = 1; __pyx_t_7 = __pyx_t_12(__pyx_t_10); if (unlikely(!__pyx_t_7)) goto __pyx_L17_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L18_unpacking_done;
__pyx_L17_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L18_unpacking_done:;
}
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
* else: output.append( k )
* elif key: output.append(k)
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_14) {
* else: output.append( "." ) # should not happen
* # snip off trailing missing data
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_14) {
*/
while (1) {
if (unlikely(((PyObject *)__pyx_v_output) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_4 = PyList_GET_SIZE(((PyObject *)__pyx_v_output)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_GET_SIZE(((PyObject *)__pyx_v_output));
__pyx_t_14 = (__pyx_t_4 > 1);
if (!__pyx_t_14) break;
* if len(last)>0: break
* output = output[:-1]
*/
- if (unlikely(((PyObject *)__pyx_v_output) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_6 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_output), -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_7 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__replace); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("enter_default_format (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
*/
if (__pyx_t_17 >= PyList_GET_SIZE(__pyx_t_14)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_16 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_17); __Pyx_INCREF(__pyx_t_16); __pyx_t_17++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_16 = PySequence_ITEM(__pyx_t_14, __pyx_t_17); __pyx_t_17++; if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_16 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_17); __Pyx_INCREF(__pyx_t_16); __pyx_t_17++;
__Pyx_XDECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_16;
__pyx_t_16 = 0;
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_18 = (__Pyx_PySequence_Contains(__pyx_t_16, __pyx_t_13, Py_NE)); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_13, __pyx_t_16))); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
if (__pyx_t_18) {
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_header (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* if value == "VCFv3.3":
* self._version = 33
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__fileformat), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__fileformat), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":523
* self._version = 33
* elif value == "VCFv4.0":
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_79), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_79), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":524
* self._version = 40
* elif value == "VCFv4.1":
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_80), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_80), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":526
* # AH - for testing
* self._version = 40
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_81), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_81), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":529
* f = self.parse_format(line, value)
* self._info[ f.id ] = f
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__INFO), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__INFO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":533
* f = self.parse_format(line, value, filter=True)
* self._filter[ f.id ] = f
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":536
* f = self.parse_format(line, value)
* self._format[ f.id ] = f
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__FORMAT), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__FORMAT), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
/* "pysam/cvcf.pyx":539
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write_header (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_t_7 = NULL;
PyObject *(*__pyx_t_8)(PyObject *);
Py_ssize_t __pyx_t_9;
- Py_ssize_t __pyx_t_10;
+ PyObject *__pyx_t_10 = NULL;
int __pyx_t_11;
- int __pyx_t_12;
- PyObject *__pyx_t_13 = NULL;
- PyObject *__pyx_t_14 = NULL;
+ PyObject *__pyx_t_12 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
for (;;) {
if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++;
} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++;
} else {
__pyx_t_4 = __pyx_t_6(__pyx_t_2);
if (unlikely(!__pyx_t_4)) {
}
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_3 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_3);
- #else
- __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_7 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
index = 1; __pyx_t_3 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L6_unpacking_done;
__pyx_L5_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_8 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L6_unpacking_done:;
}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = PyList_GET_ITEM(sequence, 0);
__pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_1);
- #else
- __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else
- {
+ } else {
Py_ssize_t index = -1;
__pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
index = 1; __pyx_t_1 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L9_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L10_unpacking_done;
__pyx_L9_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_8 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L10_unpacking_done:;
}
*
*
*/
- __pyx_t_9 = 0;
- if (unlikely(__pyx_v_var == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = __Pyx_dict_iterator(__pyx_v_var, 0, ((PyObject *)__pyx_n_s__itervalues), (&__pyx_t_10), (&__pyx_t_11)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_var, __pyx_n_s__itervalues); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_2);
- __pyx_t_2 = __pyx_t_1;
- __pyx_t_1 = 0;
- while (1) {
- __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_2, __pyx_t_10, &__pyx_t_9, NULL, &__pyx_t_1, NULL, __pyx_t_11);
- if (unlikely(__pyx_t_12 == 0)) break;
- if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_9 = 0;
+ __pyx_t_6 = NULL;
+ } else {
+ __pyx_t_9 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ }
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ for (;;) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++;
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++;
+ } else {
+ __pyx_t_1 = __pyx_t_6(__pyx_t_2);
+ if (unlikely(!__pyx_t_1)) {
+ if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ break;
+ }
+ __Pyx_GOTREF(__pyx_t_1);
+ }
__Pyx_XDECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_13));
- __pyx_t_14 = PyObject_RichCompare(__pyx_v_label, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__filter), __pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_10 = PyDict_New(); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+ __pyx_t_11 = __Pyx_PyString_Equals(__pyx_v_label, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyBool_FromLong(__pyx_t_11); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
+ if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__filter), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
+ __pyx_t_12 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(2); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_label);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_v_label);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_label);
__Pyx_GIVEREF(__pyx_v_label);
- PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_14));
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_14));
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_12);
+ __Pyx_GIVEREF(__pyx_t_12);
+ __pyx_t_12 = 0;
+ __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_12));
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_12));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_12));
+ __pyx_t_12 = 0;
+ __pyx_t_12 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_13);
- __Pyx_XDECREF(__pyx_t_14);
+ __Pyx_XDECREF(__pyx_t_10);
+ __Pyx_XDECREF(__pyx_t_12);
__Pyx_AddTraceback("pysam.cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_heading (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++;
} else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++;
} else {
__pyx_t_7 = __pyx_t_8(__pyx_t_1);
if (unlikely(!__pyx_t_7)) {
__pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (!__pyx_t_6) {
__pyx_t_10 = PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_10, __pyx_v_s, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_10, __pyx_v_s, Py_NE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
for (;;) {
if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_11)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
} else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_11)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
} else {
__pyx_t_10 = __pyx_t_8(__pyx_t_11);
if (unlikely(!__pyx_t_10)) {
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- if (unlikely(__Pyx_PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write_heading (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_GTstring = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTstring,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("convertGT (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTstring,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTstring)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTstring);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_v_gts = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
* try:
* gts = gtsRegEx.split(GTstring)
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
- PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_9));
+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
goto __pyx_L3;
}
* if len(gts) == 1: return [int(gts[0])]
* if len(gts) != 2: raise ValueError()
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__gtsRegEx); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__gtsRegEx); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_GTstring);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_GTstring);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_GTstring);
__Pyx_GIVEREF(__pyx_v_GTstring);
- __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_v_gts = __pyx_t_7;
__pyx_t_7 = 0;
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
*/
__pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_2 = (__pyx_t_8 == 1);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_t_8 == 1);
+ if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L8_try_return;
goto __pyx_L12;
}
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
*/
__pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_2 = (__pyx_t_8 != 2);
- if (__pyx_t_2) {
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_Raise(__pyx_t_1, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = (__pyx_t_8 != 2);
+ if (__pyx_t_1) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
goto __pyx_L13;
}
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
* except ValueError:
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_2) {
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_1) {
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_10 = __pyx_t_9;
} else {
- __pyx_t_10 = __pyx_t_2;
+ __pyx_t_10 = __pyx_t_1;
}
if (__pyx_t_10) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_8 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_12 = PyList_New(3); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_12);
- PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
PyList_SET_ITEM(__pyx_t_12, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
PyList_SET_ITEM(__pyx_t_12, 2, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_1 = 0;
+ __pyx_t_2 = 0;
__pyx_t_7 = 0;
__pyx_t_6 = 0;
__pyx_r = ((PyObject *)__pyx_t_12);
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_12);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyList_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_12);
__Pyx_GIVEREF(__pyx_t_12);
- PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_6);
+ PyList_SET_ITEM(__pyx_t_2, 1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- PyList_SET_ITEM(__pyx_t_1, 2, __pyx_t_7);
+ PyList_SET_ITEM(__pyx_t_2, 2, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_12 = 0;
__pyx_t_6 = 0;
__pyx_t_7 = 0;
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L8_try_return;
}
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":592
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
__pyx_t_13 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_13) {
__Pyx_AddTraceback("pysam.cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_r = ((PyObject *)__pyx_t_15);
__pyx_t_15 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L7_except_return;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L5_exception_handled;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_12);
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
CYTHON_UNUSED PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_GTdata = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTdata,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("convertGTback (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTdata,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTdata)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTdata);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_v_value = 0;
PyObject *__pyx_v_formatdict = 0;
PyObject *__pyx_v_line = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__formatdict,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_formatdata (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__formatdict,&__pyx_n_s__line,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[4])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* self._add_definition(formatdict, key, value, line )
* f = formatdict[key]
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
/* "pysam/cvcf.pyx":606
*/
__pyx_t_4 = (__pyx_v_value != Py_None);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_96); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_96); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L5;
}
__pyx_L5:;
* # deal with trailing data in some early VCF files
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
goto __pyx_L4;
}
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_values = __pyx_t_3;
__pyx_t_3 = 0;
*/
__pyx_t_3 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_3, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (!((int)__pyx_t_4)) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_3, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = ((int)__pyx_t_5);
} else {
__pyx_t_6 = ((int)__pyx_t_4);
if (__pyx_t_6) {
__pyx_t_3 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__find); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__find); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_int_neg_1, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_int_neg_1, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_8 = __pyx_t_5;
} else {
__pyx_t_8 = __pyx_t_6;
* values[-1] = values[-1].split(';')[0]
* if f.type == "Integer":
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_TRAILING_DATA); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
__pyx_t_3 = 0;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "pysam/cvcf.pyx":612
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
* if f.type == "Integer":
* for idx,v in enumerate(values):
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_1, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__Pyx_SetItemInt(__pyx_v_values, -1, __pyx_t_9, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L6;
*/
__pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_6) {
/* "pysam/cvcf.pyx":614
* if v == ".": values[idx] = f.missingvalue
*/
__Pyx_INCREF(__pyx_int_0);
- __pyx_t_2 = __pyx_int_0;
+ __pyx_t_9 = __pyx_int_0;
if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
- __pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0;
+ __pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_7 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ __pyx_t_7 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_10 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
- if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
- if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
} else {
- __pyx_t_1 = __pyx_t_10(__pyx_t_9);
- if (unlikely(!__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_10(__pyx_t_1);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_1;
- __pyx_t_1 = 0;
- __Pyx_INCREF(__pyx_t_2);
+ __pyx_v_v = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __Pyx_INCREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_v_idx);
- __pyx_v_idx = __pyx_t_2;
- __pyx_t_1 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2);
- __pyx_t_2 = __pyx_t_1;
- __pyx_t_1 = 0;
-
+ __pyx_v_idx = __pyx_t_9;
+ __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_9);
+ __pyx_t_9 = __pyx_t_2;
+ __pyx_t_2 = 0;
+
/* "pysam/cvcf.pyx":615
* if f.type == "Integer":
* for idx,v in enumerate(values):
* else: values[idx] = int(v)
* except:
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
if (__pyx_t_6) {
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L18;
}
/*else*/ {
* except:
* self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_v);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_v);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_v);
__Pyx_GIVEREF(__pyx_v_v);
- __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
}
__Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
goto __pyx_L17_try_end;
__pyx_L10_error:;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "pysam/cvcf.pyx":618
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_1, &__pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_14);
/* "pysam/cvcf.pyx":619
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L13_except_return;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L11_exception_handled;
}
__pyx_L17_try_end:;
}
}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":621
* self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
* self._line = line
* if f.id == "GT": values = list(map( self.convertGT, values ))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__String), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__String), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_6) {
*/
__pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__GT), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__GT), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_6) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGT); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_values);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_values);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_values);
__Pyx_GIVEREF(__pyx_v_values);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_v_values);
- __pyx_v_values = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_values = __pyx_t_9;
+ __pyx_t_9 = 0;
goto __pyx_L21;
}
__pyx_L21:;
* for v in values:
* if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__Character), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Character), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_6) {
for (;;) {
if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++;
} else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++;
} else {
- __pyx_t_2 = __pyx_t_10(__pyx_t_9);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_1 = __pyx_t_10(__pyx_t_9);
+ if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_1);
}
__Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_v = __pyx_t_1;
+ __pyx_t_1 = 0;
/* "pysam/cvcf.pyx":628
* elif f.type == "Character":
__pyx_t_19 = PyObject_Length(__pyx_v_v); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = (__pyx_t_19 != 1);
if (__pyx_t_6) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_101); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
__pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L24;
}
*/
__pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_14 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
if (__pyx_t_6) {
/* "pysam/cvcf.pyx":631
* try: return list(map(float,values))
*/
__Pyx_INCREF(__pyx_int_0);
- __pyx_t_14 = __pyx_int_0;
+ __pyx_t_9 = __pyx_int_0;
if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
- __pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0;
+ __pyx_t_14 = __pyx_v_values; __Pyx_INCREF(__pyx_t_14); __pyx_t_7 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ __pyx_t_7 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_10 = Py_TYPE(__pyx_t_14)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
- if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
- if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_14)) {
+ if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_14)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_14)) {
+ if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
} else {
- __pyx_t_1 = __pyx_t_10(__pyx_t_9);
- if (unlikely(!__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_10(__pyx_t_14);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_1;
- __pyx_t_1 = 0;
- __Pyx_INCREF(__pyx_t_14);
+ __pyx_v_v = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __Pyx_INCREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_v_idx);
- __pyx_v_idx = __pyx_t_14;
- __pyx_t_1 = PyNumber_Add(__pyx_t_14, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_14);
- __pyx_t_14 = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_idx = __pyx_t_9;
+ __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_9);
+ __pyx_t_9 = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":632
* elif f.type == "Float":
* try: return list(map(float,values))
* except:
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_6) {
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L27;
}
__pyx_L27:;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":633
* for idx,v in enumerate(values):
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_14 = PyTuple_New(2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyFloat_Type))));
- PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)((PyObject*)(&PyFloat_Type))));
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyFloat_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyFloat_Type))));
__Pyx_INCREF(__pyx_v_values);
- PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_v_values);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_values);
__Pyx_GIVEREF(__pyx_v_values);
- __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __pyx_t_14 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
__Pyx_GOTREF(__pyx_t_14);
- PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __pyx_r = __pyx_t_9;
- __pyx_t_9 = 0;
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_r = __pyx_t_14;
+ __pyx_t_14 = 0;
goto __pyx_L32_try_return;
}
__Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
/* "pysam/cvcf.pyx":634
* if v == ".": values[idx] = f.missingvalue
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_14, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ if (__Pyx_GetException(&__pyx_t_14, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_14);
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_2);
/* "pysam/cvcf.pyx":635
* try: return list(map(float,values))
* return [0.0] * len(values)
* else:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GIVEREF(((PyObject *)__pyx_t_17));
__pyx_t_3 = 0;
__pyx_t_17 = 0;
- __pyx_t_17 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_17 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_17);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0;
__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
__pyx_r = ((PyObject *)__pyx_t_18);
__pyx_t_18 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L31_except_return;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L29_exception_handled;
}
__pyx_L30_except_error:;
*
* def inregion(self, chrom, pos):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_14 = PyTuple_New(2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
}
__pyx_L7:;
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_chrom = 0;
PyObject *__pyx_v_pos = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__chrom,&__pyx_n_s__pos,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("inregion (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__chrom,&__pyx_n_s__pos,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
} else {
__pyx_t_1 = __pyx_t_6(__pyx_t_4);
if (unlikely(!__pyx_t_1)) {
*/
__pyx_t_1 = __Pyx_GetItemInt(__pyx_v_r, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_3) {
__pyx_t_7 = __Pyx_GetItemInt(__pyx_v_r, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
__pyx_t_8 = __Pyx_GetItemInt(__pyx_v_r, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_lineparse = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__lineparse,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_data (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__lineparse,0};
PyObject* values[3] = {0,0,0};
__pyx_defaults4 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_self);
values[2] = __pyx_dynamic_args->__pyx_arg_lineparse;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
} else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
__pyx_generator->resume_label = -1;
- __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
* # implement filtering
*/
if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_5) {
* self.error(line,self.MISSING_REF)
* if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_ref, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_14 = __Pyx_PyString_Equals(__pyx_v_ref, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
/* "pysam/cvcf.pyx":676
*/
__pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else {
__pyx_t_8 = __pyx_t_15(__pyx_t_2);
if (unlikely(!__pyx_t_8)) {
* if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
*
*/
- __pyx_t_14 = (__Pyx_PySequence_Contains(__pyx_v_c, ((PyObject *)__pyx_n_s__ACGTN), Py_NE)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = (__Pyx_NegateNonNeg(PySequence_Contains(((PyObject *)__pyx_n_s__ACGTN), __pyx_v_c))); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
__pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
*
* # make sure reference is sane
*/
- __pyx_t_14 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__N), __pyx_v_ref, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = ((PySequence_Contains(__pyx_v_ref, ((PyObject *)__pyx_n_s__N)))); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
__pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_16 = 0;
__pyx_t_2 = PyInt_FromLong(__pyx_t_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = __pyx_t_8;
- __Pyx_INCREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_v_left = __pyx_t_8;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_v_left = __pyx_t_9;
- __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":687
* if self._reference:
* faref = faref_leftflank[pos-left:]
* if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
*/
- __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_left);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
__pyx_t_10 = 0;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_v_faref_leftflank = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_faref_leftflank = __pyx_t_9;
+ __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":688
* left = max(0,pos-100)
* if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
* ref = faref
*/
- __pyx_t_8 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_8); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_faref_leftflank, __pyx_t_4, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_v_faref = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_faref_leftflank, __pyx_t_4, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_v_faref = __pyx_t_9;
+ __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":689
* faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
* ref = faref
*
*/
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_9 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_14) {
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__WRONG_REF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_faref);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_faref);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_faref);
__Pyx_GIVEREF(__pyx_v_faref);
__Pyx_INCREF(__pyx_v_ref);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_ref);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_ref);
__Pyx_GIVEREF(__pyx_v_ref);
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_9, 2, ((PyObject *)__pyx_t_10));
+ PyTuple_SET_ITEM(__pyx_t_8, 2, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_2 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L25;
}
*/
__pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_14) {
- __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
- __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_9);
- __pyx_t_9 = 0;
+ __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
+ __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_10);
+ __pyx_t_10 = 0;
goto __pyx_L26;
}
/*else*/ {
*
* if cols[5] == ".": qual = -1
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_GIVEREF(__pyx_t_10);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_10;
+ __pyx_t_10 = 0;
}
__pyx_L26:;
* else:
* try: qual = float(cols[5])
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_14) {
__pyx_v_qual = -1.0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":699
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_GOTREF(__pyx_t_9);
__Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L29_exception_handled;
}
__pyx_L30_except_error:;
* else: filter = cols[6].split(';')
*
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (!__pyx_t_14) {
__pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__PASS), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__PASS), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (!__pyx_t_5) {
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_kp_s__0), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_18 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_18 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s__0), Py_EQ); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_19 = __pyx_t_18;
} else {
*/
__pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_NE); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_5) {
/* "pysam/cvcf.pyx":708
* elts = blurp.split('=')
* if len(elts) == 1: v = None
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
- __pyx_t_9 = __pyx_t_8; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
+ __pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++;
} else {
- __pyx_t_8 = __pyx_t_15(__pyx_t_9);
- if (unlikely(!__pyx_t_8)) {
+ __pyx_t_9 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_9);
}
__Pyx_XDECREF(__pyx_v_blurp);
- __pyx_v_blurp = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_blurp = __pyx_t_9;
+ __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":709
* if cols[7] != ".":
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_v_elts);
__pyx_v_elts = __pyx_t_10;
__pyx_t_10 = 0;
*/
__pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
}
__pyx_L42:;
* v,
* self._info,
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GIVEREF(__pyx_v_line);
__pyx_t_7 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
/* "pysam/cvcf.pyx":713
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L39;
}
__pyx_L39:;
* else: format = cols[8].split(':')
*
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_1), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_kp_s_1), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_5) {
- __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_v_format = ((PyObject *)__pyx_t_10);
- __pyx_t_10 = 0;
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_v_format = ((PyObject *)__pyx_t_8);
+ __pyx_t_8 = 0;
goto __pyx_L43;
}
/*else*/ {
*
* # check: all filters are defined
*/
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__split); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_111), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_111), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_v_format = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_format = __pyx_t_8;
+ __pyx_t_8 = 0;
}
__pyx_L43:;
*
*/
if (PyList_CheckExact(__pyx_v_filter) || PyTuple_CheckExact(__pyx_v_filter)) {
- __pyx_t_10 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0;
+ __pyx_t_8 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
} else {
- __pyx_t_9 = __pyx_t_15(__pyx_t_10);
- if (unlikely(!__pyx_t_9)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_f);
- __pyx_v_f = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_f = __pyx_t_10;
+ __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":724
* # check: all filters are defined
*
* # check: format fields are defined
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_9, Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_10, __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FILTER_NOT_DEFINED); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L46;
}
__pyx_L46:;
}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":727
*
* for f in format:
* if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_5) {
/* "pysam/cvcf.pyx":728
*
*/
if (PyList_CheckExact(__pyx_v_format) || PyTuple_CheckExact(__pyx_v_format)) {
- __pyx_t_10 = __pyx_v_format; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0;
+ __pyx_t_8 = __pyx_v_format; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
} else {
- __pyx_t_1 = __pyx_t_15(__pyx_t_10);
+ __pyx_t_1 = __pyx_t_15(__pyx_t_8);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_1, Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_1, __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L50;
}
__pyx_L50:;
}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L47;
}
__pyx_L47:;
* if len(ref) != 1: self.error(line,self.V33_BAD_REF)
* newalts = []
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_5) {
/* "pysam/cvcf.pyx":733
__pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_4 != 1);
if (__pyx_t_5) {
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_REF); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_REF); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L52;
}
__pyx_L52:;
* have_deletions = False
* for a in alt:
*/
- __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_v_newalts = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_v_newalts = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":735
* if len(ref) != 1: self.error(line,self.V33_BAD_REF)
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_10 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0;
+ __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
} else {
- __pyx_t_9 = __pyx_t_15(__pyx_t_10);
- if (unlikely(!__pyx_t_9)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_a = __pyx_t_10;
+ __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":737
* have_deletions = False
__pyx_t_3 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_3 == 1);
if (__pyx_t_5) {
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyNumber_Add(__pyx_v_a, __pyx_t_10); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyNumber_Add(__pyx_v_a, __pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_a = __pyx_t_9;
+ __pyx_t_9 = 0;
goto __pyx_L55;
}
* elif a.startswith('D'): # allow D<seq> and D<num>
* have_deletions = True
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_1 = PyNumber_Add(__pyx_t_9, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_10, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyNumber_Add(__pyx_t_1, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_a = __pyx_t_10;
+ __pyx_t_10 = 0;
goto __pyx_L55;
}
* have_deletions = True
* try:
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_113), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_113), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_5) {
/* "pysam/cvcf.pyx":740
* if len(ref) < l: # add to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
*/
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_l = __pyx_t_9;
+ __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":743
* try:
* ref += addns
*/
__pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_v_l, Py_LT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_v_l, Py_LT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
/* "pysam/cvcf.pyx":744
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns
*/
- __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_1 = PyNumber_Add(__pyx_v_pos, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GIVEREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_1 = 0;
- __pyx_t_8 = 0;
+ __pyx_t_9 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_addns);
__pyx_v_addns = __pyx_t_7;
__pyx_t_2 = ((PyObject *)__pyx_v_newalts); __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
for (;;) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_9); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- #endif
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_10); __pyx_t_3++;
__Pyx_XDECREF(__pyx_v_na);
- __pyx_v_na = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_na = __pyx_t_10;
+ __pyx_t_10 = 0;
__Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_i);
__pyx_v_i = __pyx_t_7;
- __pyx_t_9 = PyNumber_Add(__pyx_t_7, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyNumber_Add(__pyx_t_7, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7);
- __pyx_t_7 = __pyx_t_9;
- __pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_9);
- if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_7 = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_L56_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_20 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_20) {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_10);
/* "pysam/cvcf.pyx":749
* a = ref[l:] # new deletion, deleting pos...pos+l
* if len(ref) < len(s): # add Ns to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
*/
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_v_s);
- __pyx_v_s = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_s = __pyx_t_9;
+ __pyx_t_9 = 0;
/* "pysam/cvcf.pyx":750
* except ValueError:
* if not s.endswith(addns) and addns != 'N'*len(addns):
* self.error(line,self.V33_UNMATCHED_DELETION,
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__pyx_t_21 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__pyx_t_1 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = 0;
__pyx_t_22 = 0;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0;
__Pyx_XDECREF(__pyx_v_addns);
__pyx_v_addns = __pyx_t_1;
__Pyx_INCREF(__pyx_v_addns);
PyTuple_SET_ITEM(__pyx_t_23, 0, __pyx_v_addns);
__Pyx_GIVEREF(__pyx_v_addns);
- __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_14 = (!__pyx_t_5);
if (__pyx_t_14) {
__pyx_t_21 = PyObject_Length(__pyx_v_addns); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_23 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_8); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_23 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_9); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_23));
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_addns, ((PyObject *)__pyx_t_23), Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_addns, ((PyObject *)__pyx_t_23), Py_NE); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_19 = __pyx_t_5;
} else {
__pyx_t_19 = __pyx_t_14;
* "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
* ref += addns
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_23 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_114); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_23 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_114); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
/* "pysam/cvcf.pyx":754
* if not s.endswith(addns) and addns != 'N'*len(addns):
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_23);
- __Pyx_GIVEREF(__pyx_t_23);
+ PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_24, 2, ((PyObject *)__pyx_t_22));
__Pyx_GIVEREF(((PyObject *)__pyx_t_22));
- __pyx_t_23 = 0;
+ __pyx_t_9 = 0;
__pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_23, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
goto __pyx_L70;
__pyx_t_24 = ((PyObject *)__pyx_v_newalts); __Pyx_INCREF(__pyx_t_24); __pyx_t_21 = 0;
for (;;) {
if (__pyx_t_21 >= PyList_GET_SIZE(__pyx_t_24)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_21); __Pyx_INCREF(__pyx_t_8); __pyx_t_21++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_24, __pyx_t_21); __pyx_t_21++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- #endif
+ __pyx_t_23 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_21); __Pyx_INCREF(__pyx_t_23); __pyx_t_21++;
__Pyx_XDECREF(__pyx_v_na);
- __pyx_v_na = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_na = __pyx_t_23;
+ __pyx_t_23 = 0;
__Pyx_INCREF(__pyx_t_22);
__Pyx_XDECREF(__pyx_v_i);
__pyx_v_i = __pyx_t_22;
- __pyx_t_8 = PyNumber_Add(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_23 = PyNumber_Add(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_23);
__Pyx_DECREF(__pyx_t_22);
- __pyx_t_22 = __pyx_t_8;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_8);
- if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_22 = __pyx_t_23;
+ __pyx_t_23 = 0;
+ __pyx_t_23 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_23);
+ if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_23) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
}
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__pyx_t_22 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L57_exception_handled;
}
__pyx_L58_except_error:;
* newalts.append(a)
* alt = newalts
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
*/
__pyx_t_25 = PyList_Append(__pyx_v_newalts, __pyx_v_a); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":761
* self.error(line,self.V33_BAD_ALLELE)
* # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
* addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
*/
- __pyx_t_10 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_19) {
/* "pysam/cvcf.pyx":766
* ref += addn
* alt = [allele+addn for allele in alt]
*/
- __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_10, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_INCREF(__pyx_v_chrom);
__Pyx_GIVEREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
__pyx_t_7 = 0;
__pyx_t_2 = 0;
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __pyx_v_addn = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_addn = __pyx_t_10;
+ __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":767
* # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
* alt = [allele+addn for allele in alt]
* else:
*/
- __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_ref = __pyx_t_10;
+ __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":768
* addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
* else:
* addn = get_sequence(chrom,pos-1,pos,self._reference)
*/
- __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
__pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_22, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_22, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_22);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_8 = __pyx_t_15(__pyx_t_22);
+ if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_8);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Add(__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_v_allele = __pyx_t_8;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyNumber_Add(__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ if (unlikely(PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_8))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = ((PyObject *)__pyx_t_9);
- __Pyx_INCREF(__pyx_t_22);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_10));
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(__pyx_t_22);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_22;
- __pyx_t_22 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
+ __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_10);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
goto __pyx_L74;
}
/*else*/ {
* ref = addn + ref
* alt = [addn + allele for allele in alt]
*/
- __pyx_t_22 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_22 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
__Pyx_INCREF(__pyx_v_pos);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_pos);
__Pyx_GIVEREF(__pyx_v_pos);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_t_9 = 0;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_22 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_v_addn = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_addn = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":771
* else:
* alt = [addn + allele for allele in alt]
* pos -= 1
*/
- __pyx_t_10 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_8 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_ref = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":772
* addn = get_sequence(chrom,pos-1,pos,self._reference)
* pos -= 1
* else:
*/
- __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
__pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_22 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_22 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_22 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
} else {
- __pyx_t_22 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_22)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_22;
- __pyx_t_22 = 0;
- __pyx_t_22 = PyNumber_Add(__pyx_v_addn, __pyx_v_allele); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_22))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyNumber_Add(__pyx_v_addn, __pyx_v_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = ((PyObject *)__pyx_t_10);
- __Pyx_INCREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_8));
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_2;
- __pyx_t_2 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":773
* ref = addn + ref
* else:
* # format v4.0 -- just check for nucleotides
*/
- __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_pos);
- __pyx_v_pos = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_pos = __pyx_t_8;
+ __pyx_t_8 = 0;
}
__pyx_L74:;
goto __pyx_L73;
* self.error(line,self.V40_BAD_ALLELE,allele)
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_2 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_allele = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":777
* # format v4.0 -- just check for nucleotides
* self.error(line,self.V40_BAD_ALLELE,allele)
*
*/
- __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__alleleRegEx); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__match); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__alleleRegEx); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__match); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_allele);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_allele);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_allele);
__Pyx_GIVEREF(__pyx_v_allele);
- __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_14 = (!__pyx_t_19);
if (__pyx_t_14) {
*
* # check for leading nucleotide in indel calls
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V40_BAD_ALLELE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V40_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_allele);
- PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_v_allele);
+ PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_allele);
__Pyx_GIVEREF(__pyx_v_allele);
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L81;
}
__pyx_L81:;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__pyx_L51:;
* if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_2 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_allele = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":782
* # check for leading nucleotide in indel calls
__pyx_t_3 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_3 == 0);
if (__pyx_t_14) {
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyTuple_New(2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
- __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
goto __pyx_L85;
}
__pyx_L85:;
* self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
*
*/
- __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_9, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_10, __pyx_t_22, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_14) {
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_22 = PyNumber_Add(__pyx_t_10, __pyx_t_9); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyNumber_Add(__pyx_t_2, __pyx_t_22); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_19 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__N), __pyx_t_22, Py_NE)); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_19 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_10, ((PyObject *)__pyx_n_s__N)))); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_5 = __pyx_t_19;
} else {
__pyx_t_5 = __pyx_t_14;
*
* # trim trailing bases in alleles
*/
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_116); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_116); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
+ __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L86;
}
__pyx_L86:;
}
__pyx_L84:;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":788
*
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
* break
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_b, __pyx_n_s__len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_8 = __Pyx_GetName(__pyx_b, __pyx_n_s__len); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_22 = PyTuple_New(2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_alt);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_cur_scope->__pyx_v_alt);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_cur_scope->__pyx_v_alt);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_alt);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
__pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_8, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyObject_RichCompare(__pyx_t_2, __pyx_t_10, Py_LT); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
if (__pyx_t_5) {
- __Pyx_INCREF(__pyx_t_2);
- __pyx_t_9 = __pyx_t_2;
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_22 = __pyx_t_8;
} else {
- __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_9 = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_22 = __pyx_t_10;
+ __pyx_t_10 = 0;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_int_1);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_int_1);
__Pyx_GIVEREF(__pyx_int_1);
- __Pyx_INCREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
- __pyx_t_2 = __pyx_t_9; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __Pyx_INCREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ if (PyList_CheckExact(__pyx_t_22) || PyTuple_CheckExact(__pyx_t_22)) {
+ __pyx_t_8 = __pyx_t_22; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_22 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
} else {
- __pyx_t_9 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_9)) {
+ __pyx_t_22 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_22)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_22);
}
__Pyx_XDECREF(__pyx_v_i);
- __pyx_v_i = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_i = __pyx_t_22;
+ __pyx_t_22 = 0;
/* "pysam/cvcf.pyx":790
* if alt:
* break
* ref, alt = ref[:-1], [allele[:-1] for allele in alt]
*/
- __pyx_t_9 = __pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PySet_Type))), ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __pyx_t_3 = PySet_Size(__pyx_t_9); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
+ __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_Call(((PyObject *)((PyObject*)(&PySet_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_3 = PySet_Size(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__pyx_t_5 = (__pyx_t_3 > 1);
if (!__pyx_t_5) {
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_ref, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_alt, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_ref, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_22, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_alt, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_RichCompare(__pyx_t_9, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_10, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_19 = __pyx_t_14;
} else {
__pyx_t_19 = __pyx_t_5;
*
* # left-align alleles, if a reference is available
*/
- __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_9 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_9); __pyx_t_3 = 0;
+ __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_3 = 0;
__pyx_t_26 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_26 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ __pyx_t_3 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_26 = Py_TYPE(__pyx_t_22)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_9)) {
- if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_9, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_9)) {
- if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_9, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else {
- __pyx_t_7 = __pyx_t_26(__pyx_t_9);
+ __pyx_t_7 = __pyx_t_26(__pyx_t_22);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
__pyx_t_7 = 0;
__pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = ((PyObject *)__pyx_t_10);
- __Pyx_INCREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = ((PyObject *)__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_22);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_ref = __pyx_t_10;
+ __pyx_t_10 = 0;
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_9;
- __pyx_t_9 = 0;
+ __Pyx_GIVEREF(__pyx_t_22);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_22;
+ __pyx_t_22 = 0;
}
__pyx_L89_break:;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L87;
}
__pyx_L87:;
* while left < pos:
* movable = True
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_19) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_14 = __pyx_t_5;
} else {
__pyx_t_14 = __pyx_t_19;
*/
while (1) {
if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (!__pyx_t_14) break;
/* "pysam/cvcf.pyx":797
* longest, shortest = allele, ref
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_22 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
} else {
- __pyx_t_9 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_9)) {
+ __pyx_t_22 = __pyx_t_15(__pyx_t_8);
+ if (unlikely(!__pyx_t_22)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_22);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_allele = __pyx_t_22;
+ __pyx_t_22 = 0;
/* "pysam/cvcf.pyx":799
* movable = True
* else:
* longest, shortest = ref, allele
*/
- __pyx_t_9 = __pyx_v_allele;
- __Pyx_INCREF(__pyx_t_9);
- __pyx_t_22 = __pyx_v_ref;
+ __pyx_t_22 = __pyx_v_allele;
__Pyx_INCREF(__pyx_t_22);
+ __pyx_t_10 = __pyx_v_ref;
+ __Pyx_INCREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_v_longest);
- __pyx_v_longest = __pyx_t_9;
- __pyx_t_9 = 0;
- __Pyx_XDECREF(__pyx_v_shortest);
- __pyx_v_shortest = __pyx_t_22;
+ __pyx_v_longest = __pyx_t_22;
__pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_v_shortest);
+ __pyx_v_shortest = __pyx_t_10;
+ __pyx_t_10 = 0;
goto __pyx_L98;
}
/*else*/ {
* if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
* movable = False
*/
- __pyx_t_22 = __pyx_v_ref;
+ __pyx_t_10 = __pyx_v_ref;
+ __Pyx_INCREF(__pyx_t_10);
+ __pyx_t_22 = __pyx_v_allele;
__Pyx_INCREF(__pyx_t_22);
- __pyx_t_9 = __pyx_v_allele;
- __Pyx_INCREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_v_longest);
- __pyx_v_longest = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_longest = __pyx_t_10;
+ __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_v_shortest);
- __pyx_v_shortest = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_shortest = __pyx_t_22;
+ __pyx_t_22 = 0;
}
__pyx_L98:;
__pyx_t_14 = (__pyx_t_21 == __pyx_t_3);
if (!__pyx_t_14) {
__pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_shortest, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_shortest, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_RichCompare(__pyx_t_9, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_5 = __pyx_t_19;
} else {
__pyx_t_5 = __pyx_t_14;
* movable = False
* if not movable:
*/
- __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_longest, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_longest, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_21 = (__pyx_t_3 - 1);
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_21, sizeof(Py_ssize_t), PyInt_FromSsize_t); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_22, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_21, sizeof(Py_ssize_t), PyInt_FromSsize_t); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_RichCompare(__pyx_t_10, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
if (__pyx_t_5) {
/* "pysam/cvcf.pyx":806
}
__pyx_L100:;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":807
* if longest[-1].upper() != longest[len(shortest)-1].upper():
* alt = [allele[:-1] for allele in alt]
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_ref = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":810
* break
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
* ref = faref_leftflank[pos-left-1] + ref
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_9 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
+ __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_9);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_2 = __pyx_t_15(__pyx_t_22);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
- __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_v_allele = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_2))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = ((PyObject *)__pyx_t_2);
- __Pyx_INCREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_8));
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_9;
- __pyx_t_9 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":811
* ref = ref[:-1]
* ref = faref_leftflank[pos-left-1] + ref
* alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
*/
- __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_2 = __pyx_t_15(__pyx_t_22);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_allele = __pyx_t_2;
+ __pyx_t_2 = 0;
__pyx_t_21 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_2))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_t_9));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_9));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_INCREF(((PyObject *)__pyx_t_8));
+ PyTuple_SET_ITEM(__pyx_t_22, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_RichCompare(__pyx_t_8, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
if (!__pyx_t_5) {
__pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_4 == 0);
* pos -= 1
*/
if (unlikely(!__pyx_v_faref_leftflank)) { __Pyx_RaiseUnboundLocalError("faref_leftflank"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_2 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_9); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Add(__pyx_t_2, __pyx_v_ref); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_22 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_8 = PyNumber_Subtract(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_8); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyNumber_Add(__pyx_t_22, __pyx_v_ref); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_ref = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":813
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
* pos -= 1
*
*/
- __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
+ __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_2 = __pyx_t_15(__pyx_t_22);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_allele = __pyx_t_2;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyNumber_Subtract(__pyx_t_10, __pyx_int_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_10); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_22); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_t_2, __pyx_v_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyNumber_Add(__pyx_t_10, __pyx_v_allele); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_22))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = ((PyObject *)__pyx_t_9);
- __Pyx_INCREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_INCREF(((PyObject *)__pyx_t_8));
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_2;
- __pyx_t_2 = 0;
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":814
* ref = faref_leftflank[pos-left-1] + ref
*
* # parse sample columns
*/
- __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_pos);
- __pyx_v_pos = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_pos = __pyx_t_8;
+ __pyx_t_8 = 0;
goto __pyx_L104;
}
__pyx_L104:;
* for sample in cols[9:]:
* dict = {}
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_v_samples = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_v_samples = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":818
* # parse sample columns
* dict = {}
* values = sample.split(':')
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_cols, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
- __pyx_t_9 = __pyx_t_2; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_cols, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
+ __pyx_t_22 = __pyx_t_8; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else {
- __pyx_t_2 = __pyx_t_15(__pyx_t_9);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_8 = __pyx_t_15(__pyx_t_22);
+ if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_8);
}
__Pyx_XDECREF(__pyx_v_sample);
- __pyx_v_sample = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_sample = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":819
* samples = []
* values = sample.split(':')
* if len(values) > len(format):
*/
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_XDECREF(((PyObject *)__pyx_v_dict));
- __pyx_v_dict = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_dict = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":820
* for sample in cols[9:]:
* if len(values) > len(format):
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_sample, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_22 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_sample, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_values);
- __pyx_v_values = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_values = __pyx_t_10;
+ __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":821
* dict = {}
* for idx in range(len(format)):
* expected = self.get_expected(format[idx], self._format, alt)
*/
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_18); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_18); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
- PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_sample);
PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_v_sample);
__Pyx_GIVEREF(__pyx_v_sample);
PyTuple_SET_ITEM(__pyx_t_24, 2, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_10 = 0;
+ __pyx_t_2 = 0;
__pyx_t_7 = 0;
__pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_24)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_24, 2, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_2 = 0;
+ __pyx_t_8 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L111;
for (;;) {
if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_24)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_24)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_24, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_24)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_24)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_7 = PySequence_ITEM(__pyx_t_24, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else {
__pyx_t_7 = __pyx_t_26(__pyx_t_24);
if (unlikely(!__pyx_t_7)) {
*/
__pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__get_expected); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_alt);
- PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_cur_scope->__pyx_v_alt);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_cur_scope->__pyx_v_alt);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_alt);
- __pyx_t_22 = 0;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_expected);
- __pyx_v_expected = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_expected = __pyx_t_8;
+ __pyx_t_8 = 0;
/* "pysam/cvcf.pyx":825
* for idx in range(len(format)):
* if expected == -1: value = "."
*/
__pyx_t_21 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_8, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_19) {
- __pyx_t_10 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L114;
}
/*else*/ {
* else: value = ",".join(["."]*expected)
*
*/
- __pyx_t_10 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_19) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
__Pyx_XDECREF(__pyx_v_value);
*
* dict[format[idx]] = self.parse_formatdata(format[idx],
*/
- __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyList_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_9));
+ PyList_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
- { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_8, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_temp);
- __Pyx_DECREF(__pyx_t_2);
- __pyx_t_2 = __pyx_temp;
+ __Pyx_DECREF(__pyx_t_8);
+ __pyx_t_8 = __pyx_temp;
}
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_8;
+ __pyx_t_8 = 0;
}
__pyx_L115:;
}
* value,
* self._format,
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
* line)
* if expected != -1 and len(dict[format[idx]]) != expected:
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
/* "pysam/cvcf.pyx":833
* value,
* if expected != -1 and len(dict[format[idx]]) != expected:
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
*/
- __pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_7);
+ __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
__pyx_t_7 = 0;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":830
* else: value = ",".join(["."]*expected)
* value,
* self._format,
*/
- __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_22, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_10, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":834
* self._format,
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
*/
- __pyx_t_10 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_19) {
- __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_2); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_21 = PyObject_Length(__pyx_t_10); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_t_22); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_10, __pyx_v_expected, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_14 = __pyx_t_5;
} else {
__pyx_t_14 = __pyx_t_19;
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_20); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_20); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
/* "pysam/cvcf.pyx":836
* if expected != -1 and len(dict[format[idx]]) != expected:
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
* dict[format[idx]] = dict[format[idx]][:expected]
*/
- __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_7); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_23 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_7); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_expected);
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_expected);
__Pyx_GIVEREF(__pyx_v_expected);
- PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_2 = 0;
+ PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_23);
+ __Pyx_GIVEREF(__pyx_t_23);
__pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_23 = 0;
+ __pyx_t_23 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_23));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_7, 2, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_22 = 0;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_7, 2, ((PyObject *)__pyx_t_23));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_23));
+ __pyx_t_10 = 0;
+ __pyx_t_23 = 0;
+ __pyx_t_23 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
/* "pysam/cvcf.pyx":837
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
* dict[format[idx]] = dict[format[idx]][:expected]
* samples.append( dict )
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
__pyx_t_21 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_7 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_23 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_LT); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_23); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
if (__pyx_t_14) {
- __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_2); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_10, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_22, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_t_8); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_22); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_22 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_t_22); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyList_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyList_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_8, __pyx_t_10); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_temp);
- __Pyx_DECREF(__pyx_t_2);
- __pyx_t_2 = __pyx_temp;
+ __Pyx_DECREF(__pyx_t_8);
+ __pyx_t_8 = __pyx_temp;
}
- __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyNumber_InPlaceAdd(__pyx_t_7, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyNumber_InPlaceAdd(__pyx_t_7, ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_8, __pyx_t_22) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_23, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
goto __pyx_L117;
}
__pyx_L117:;
* samples.append( dict )
*
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
__pyx_t_21 = __Pyx_PyIndex_AsSsize_t(__pyx_v_expected); if (unlikely((__pyx_t_21 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_t_22, 0, __pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_22, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_23 = __Pyx_PySequence_GetSlice(__pyx_t_10, 0, __pyx_t_21); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_23);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_10, __pyx_t_23) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
goto __pyx_L116;
}
__pyx_L116:;
*/
__pyx_t_25 = PyList_Append(__pyx_v_samples, ((PyObject *)__pyx_v_dict)); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
/* "pysam/cvcf.pyx":842
*
* 'pos':pos, # return 0-based position
* 'id':id,
*/
- __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__chrom), __pyx_v_chrom) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyDict_New(); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_22));
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__chrom), __pyx_v_chrom) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":843
* # done
* 'id':id,
* 'ref':ref,
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__pos), __pyx_v_pos) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__pos), __pyx_v_pos) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":844
* d = {'chrom':chrom,
* 'ref':ref,
* 'alt':alt,
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__id), __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__id), __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":845
* 'pos':pos, # return 0-based position
* 'alt':alt,
* 'qual':qual,
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__ref), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__ref), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":846
* 'id':id,
* 'qual':qual,
* 'filter':filter,
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__alt), __pyx_cur_scope->__pyx_v_alt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__alt), __pyx_cur_scope->__pyx_v_alt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":847
* 'ref':ref,
*/
__pyx_t_24 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__qual), __pyx_t_24) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__qual), __pyx_t_24) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
/* "pysam/cvcf.pyx":848
* 'info':info,
* 'format':format}
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__filter), __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__filter), __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":849
* 'qual':qual,
* 'format':format}
* for key,value in zip(self._samples,samples):
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_v_info)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_v_info)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/cvcf.pyx":850
* 'filter':filter,
* for key,value in zip(self._samples,samples):
* d[key] = value
*/
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__format), __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_d = __pyx_t_9;
- __pyx_t_9 = 0;
+ if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__format), __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_d = __pyx_t_22;
+ __pyx_t_22 = 0;
/* "pysam/cvcf.pyx":851
* 'info':info,
* d[key] = value
*
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
- PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
__Pyx_INCREF(((PyObject *)__pyx_v_samples));
PyTuple_SET_ITEM(__pyx_t_24, 1, ((PyObject *)__pyx_v_samples));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samples));
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
- if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
- __pyx_t_24 = __pyx_t_9; __Pyx_INCREF(__pyx_t_24); __pyx_t_4 = 0;
+ if (PyList_CheckExact(__pyx_t_22) || PyTuple_CheckExact(__pyx_t_22)) {
+ __pyx_t_24 = __pyx_t_22; __Pyx_INCREF(__pyx_t_24); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
__pyx_t_15 = Py_TYPE(__pyx_t_24)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_24)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_24)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_24, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_22 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_24)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_24)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_24, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
} else {
- __pyx_t_9 = __pyx_t_15(__pyx_t_24);
- if (unlikely(!__pyx_t_9)) {
+ __pyx_t_22 = __pyx_t_15(__pyx_t_24);
+ if (unlikely(!__pyx_t_22)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_22);
}
- if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
- PyObject* sequence = __pyx_t_9;
- #if CYTHON_COMPILING_IN_CPYTHON
- Py_ssize_t size = Py_SIZE(sequence);
- #else
- Py_ssize_t size = PySequence_Size(sequence);
- #endif
- if (unlikely(size != 2)) {
- if (size > 2) __Pyx_RaiseTooManyValuesError(2);
- else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
+ if ((likely(PyTuple_CheckExact(__pyx_t_22))) || (PyList_CheckExact(__pyx_t_22))) {
+ PyObject* sequence = __pyx_t_22;
if (likely(PyTuple_CheckExact(sequence))) {
- __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_22 = PyTuple_GET_ITEM(sequence, 1);
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
+ if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_23 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
- __pyx_t_8 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_22 = PyList_GET_ITEM(sequence, 1);
+ if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
+ if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_23 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_8);
- __Pyx_INCREF(__pyx_t_22);
- #else
- __pyx_t_8 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_22 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else
- {
+ __Pyx_INCREF(__pyx_t_23);
+ __Pyx_INCREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ } else {
Py_ssize_t index = -1;
- __pyx_t_2 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_27 = Py_TYPE(__pyx_t_2)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_27(__pyx_t_2); if (unlikely(!__pyx_t_8)) goto __pyx_L120_unpacking_failed;
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_22 = __pyx_t_27(__pyx_t_2); if (unlikely(!__pyx_t_22)) goto __pyx_L120_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_22);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_27(__pyx_t_2), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_27 = NULL;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_27 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ index = 0; __pyx_t_23 = __pyx_t_27(__pyx_t_8); if (unlikely(!__pyx_t_23)) goto __pyx_L120_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_23);
+ index = 1; __pyx_t_10 = __pyx_t_27(__pyx_t_8); if (unlikely(!__pyx_t_10)) goto __pyx_L120_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_10);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_27(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L121_unpacking_done;
__pyx_L120_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_27 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L121_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_key);
- __pyx_v_key = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_key = __pyx_t_23;
+ __pyx_t_23 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_value = __pyx_t_10;
+ __pyx_t_10 = 0;
/* "pysam/cvcf.pyx":852
* 'format':format}
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
PyObject *__pyx_v_data = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__data,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write_data (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__data,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_3)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_3)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_3);
if (unlikely(!__pyx_t_2)) {
* if data['alt'] == []: alt = "."
* else: alt = ",".join(data['alt'])
*/
- __pyx_t_6 = (__Pyx_PySequence_Contains(__pyx_v_k, __pyx_v_data, Py_NE)); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_data, __pyx_v_k))); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_6) {
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
*/
__pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
*/
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
*/
__pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__qual)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_11)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_11)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_8 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
} else {
__pyx_t_8 = __pyx_t_5(__pyx_t_11);
if (unlikely(!__pyx_t_8)) {
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_parse_header (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
} else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_stream = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_parse (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__stream,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_5)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_5)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_5)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_5);
if (unlikely(!__pyx_t_2)) {
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
__pyx_generator->resume_label = -1;
- __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getsamples (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_41getsamples(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_samples = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__samples,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setsamples (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__samples,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samples)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samples);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getheader (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_45getheader(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_header = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__header,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setheader (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__header,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getinfo (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_49getinfo(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_info = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__info,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setinfo (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__info,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__info)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__info);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getformat (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_53getformat(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_format = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setformat (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getfilter (wrapper)", 0);
+ __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_57getfilter(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filter = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filter,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setfilter (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filter,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filter)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filter);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_version = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setversion (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__version)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__version);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* self._version = version
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_33, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_33, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_40, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_40, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __pyx_t_3;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_regions = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__regions,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setregions (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__regions,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__regions)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__regions);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_ref = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__ref,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setreference (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__ref,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_errorstring = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("ignoreerror (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_errorstring = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("warnerror (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
PyObject *__pyx_v_datagenerator = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__datagenerator,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__datagenerator,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__datagenerator)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__datagenerator);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("writeheader (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_v_pos2 = 0;
PyObject *__pyx_v_ref2 = 0;
PyObject *__pyx_v_alt2 = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("compare_calls (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0};
PyObject* values[7] = {0,0,0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2)) != 0)) kw_args--;
+ values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2);
+ if (likely(values[4])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
- if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2)) != 0)) kw_args--;
+ values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2);
+ if (likely(values[5])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 6:
- if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2)) != 0)) kw_args--;
+ values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2);
+ if (likely(values[6])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
* # from both calls, trim rightmost bases when identical. Do this safely, i.e.
* # only when the reference bases are not Ns
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt2, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
* ###########################################################################################################
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("connect (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[5] = {0,0,0,0,0};
/* "pysam/cvcf.pyx":1022
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
CYTHON_UNUSED PyObject *__pyx_v_self = 0;
CYTHON_UNUSED PyObject *__pyx_v_record = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("validate (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
static void __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->vcf);
- PyObject_GC_Track(o);
- if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord);
+ Py_XDECREF(p->vcf);
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o);
}
static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
- e = ((likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) ? ((__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) ? __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_VCFRecord)); if (e) return e;
+ if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) {
+ e = __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->vcf) {
e = (*v)(p->vcf, a); if (e) return e;
}
static int __pyx_tp_clear_5pysam_4cvcf_VCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) { if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_VCFRecord);
+ if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) {
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o);
+ }
tmp = ((PyObject*)p->vcf);
p->vcf = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return r;
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o);
}
static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->vcffile);
- PyObject_GC_Track(o);
- if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord);
+ Py_XDECREF(p->vcffile);
+ __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o);
}
static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
- e = ((likely(__pyx_ptype_5pysam_6ctabix_Parser)) ? ((__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord)); if (e) return e;
+ if (__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) {
+ e = __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->vcffile) {
e = (*v)(p->vcffile, a); if (e) return e;
}
static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) { if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_asVCFRecord);
+ if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) {
+ __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o);
+ }
tmp = ((PyObject*)p->vcffile);
p->vcffile = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_v_alt);
- PyObject_GC_Track(o);
+ Py_XDECREF(p->__pyx_v_alt);
(*Py_TYPE(o)->tp_free)(o);
}
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_outer_scope);
- Py_CLEAR(p->__pyx_v_allele);
- Py_CLEAR(p->__pyx_t_0);
- PyObject_GC_Track(o);
+ Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+ Py_XDECREF(p->__pyx_v_allele);
+ Py_XDECREF(p->__pyx_t_0);
(*Py_TYPE(o)->tp_free)(o);
}
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_v_d);
- Py_CLEAR(p->__pyx_v_line);
- Py_CLEAR(p->__pyx_v_self);
- Py_CLEAR(p->__pyx_v_stream);
- Py_CLEAR(p->__pyx_t_1);
- PyObject_GC_Track(o);
+ Py_XDECREF(p->__pyx_v_d);
+ Py_XDECREF(p->__pyx_v_line);
+ Py_XDECREF(p->__pyx_v_self);
+ Py_XDECREF(p->__pyx_v_stream);
+ Py_XDECREF(p->__pyx_t_1);
(*Py_TYPE(o)->tp_free)(o);
}
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if PY_MAJOR_VERSION >= 3
- {
- PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!PyDict_GetItemString(modules, "pysam.cvcf")) {
- if (unlikely(PyDict_SetItemString(modules, "pysam.cvcf", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- }
- #endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
#endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
+ PyString_AS_STRING(kw_name));
#endif
}
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
}
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
+ if (*name) {
values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
+ } else {
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
}
}
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
return -1;
}
+
+
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
*type = local_type;
*value = local_value;
*tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
+ 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_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
+ these objects (XDECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
return 0;
bad:
*type = 0;
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ 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;
+ }
+ if (value == NULL) {
+ value = Py_None;
Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
}
#if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
+ if (!PyClass_Check(type))
#else
- if (PyType_Check(type)) {
+ if (!PyType_Check(type))
#endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
+ {
+ if (value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
+ Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
+ } else if (!PyExceptionClass_Check(type)) {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause && cause != Py_None) {
+ if (cause) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
"BaseException");
goto bad;
}
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
}
}
bad:
- Py_XDECREF(owned_instance);
return;
}
#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
-#if CYTHON_COMPILING_IN_PYPY
- float_value = PyNumber_Float(obj);
-#else
if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
return PyFloat_AsDouble(obj);
} else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
PyTuple_SET_ITEM(args, 0, 0);
Py_DECREF(args);
}
-#endif
if (likely(float_value)) {
double value = PyFloat_AS_DOUBLE(float_value);
Py_DECREF(float_value);
return (double)-1;
}
-static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
- PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
+ PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ index, (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else {
- return __Pyx_IterFinish();
+ } else if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
}
return 0;
}
return q;
}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
- if (t == Py_None) {
- __Pyx_RaiseNoneNotIterableError();
- } else if (PyTuple_GET_SIZE(t) < index) {
- __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
- } else {
- __Pyx_RaiseTooManyValuesError(index);
- }
-}
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
- int is_tuple, int has_known_size, int decref_tuple) {
- Py_ssize_t index;
- PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
- if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
- iternextfunc iternext;
- iter = PyObject_GetIter(tuple);
- if (unlikely(!iter)) goto bad;
- if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
- iternext = Py_TYPE(iter)->tp_iternext;
- value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
- value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
- if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
- Py_DECREF(iter);
- } else {
- if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
- __Pyx_UnpackTupleError(tuple, 2);
- goto bad;
- }
-#if CYTHON_COMPILING_IN_PYPY
- value1 = PySequence_ITEM(tuple, 0);
- if (unlikely(!value1)) goto bad;
- value2 = PySequence_ITEM(tuple, 1);
- if (unlikely(!value2)) goto bad;
-#else
- value1 = PyTuple_GET_ITEM(tuple, 0);
- value2 = PyTuple_GET_ITEM(tuple, 1);
- Py_INCREF(value1);
- Py_INCREF(value2);
-#endif
- if (decref_tuple) { Py_DECREF(tuple); }
- }
- *pvalue1 = value1;
- *pvalue2 = value2;
- return 0;
-unpacking_failed:
- if (!has_known_size && __Pyx_IterFinish() == 0)
- __Pyx_RaiseNeedMoreValuesError(index);
-bad:
- Py_XDECREF(iter);
- Py_XDECREF(value1);
- Py_XDECREF(value2);
- if (decref_tuple) { Py_XDECREF(tuple); }
- return -1;
-}
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
- Py_ssize_t* p_orig_length, int* p_source_is_dict) {
- is_dict = is_dict || likely(PyDict_CheckExact(iterable));
- *p_source_is_dict = is_dict;
-#if !CYTHON_COMPILING_IN_PYPY
- if (is_dict) {
- *p_orig_length = PyDict_Size(iterable);
- Py_INCREF(iterable);
- return iterable;
- }
-#endif
- *p_orig_length = 0;
- if (method_name) {
- PyObject* iter;
- iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL);
- if (!iterable)
- return NULL;
-#if !CYTHON_COMPILING_IN_PYPY
- if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
- return iterable;
-#endif
- iter = PyObject_GetIter(iterable);
- Py_DECREF(iterable);
- return iter;
- }
- return PyObject_GetIter(iterable);
-}
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
- PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
- PyObject* next_item;
-#if !CYTHON_COMPILING_IN_PYPY
- if (source_is_dict) {
- PyObject *key, *value;
- if (unlikely(orig_length != PyDict_Size(iter_obj))) {
- PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
- return -1;
- }
- if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
- return 0;
- }
- if (pitem) {
- PyObject* tuple = PyTuple_New(2);
- if (unlikely(!tuple)) {
- return -1;
- }
- Py_INCREF(key);
- Py_INCREF(value);
- PyTuple_SET_ITEM(tuple, 0, key);
- PyTuple_SET_ITEM(tuple, 1, value);
- *pitem = tuple;
- } else {
- if (pkey) {
- Py_INCREF(key);
- *pkey = key;
- }
- if (pvalue) {
- Py_INCREF(value);
- *pvalue = value;
- }
- }
- return 1;
- } else if (PyTuple_CheckExact(iter_obj)) {
- Py_ssize_t pos = *ppos;
- if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
- *ppos = pos + 1;
- next_item = PyTuple_GET_ITEM(iter_obj, pos);
- Py_INCREF(next_item);
- } else if (PyList_CheckExact(iter_obj)) {
- Py_ssize_t pos = *ppos;
- if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
- *ppos = pos + 1;
- next_item = PyList_GET_ITEM(iter_obj, pos);
- Py_INCREF(next_item);
- } else
-#endif
- {
- next_item = PyIter_Next(iter_obj);
- if (unlikely(!next_item)) {
- return __Pyx_IterFinish();
- }
- }
- if (pitem) {
- *pitem = next_item;
- } else if (pkey && pvalue) {
- if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
- return -1;
- } else if (pkey) {
- *pkey = next_item;
- } else {
- *pvalue = next_item;
- }
- return 1;
-}
static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
}
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_dealloc != current_tp_dealloc)
- type = type->tp_base;
- while (type && type->tp_dealloc == current_tp_dealloc)
- type = type->tp_base;
- if (type)
- type->tp_dealloc(obj);
-}
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- while (type && type->tp_traverse == current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_traverse)
- return type->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- while (type && type->tp_clear == current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_clear)
- type->tp_clear(obj);
-}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
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);
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
+ /* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
PyString_AsString(func_name), (void *)op);
#endif
}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
+ __Pyx_PyCFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
+static int __Pyx_CyFunction_init(void)
+{
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
+void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
+{
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults = PyMem_Malloc(size);
if (!m->defaults)
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
+{
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults_tuple = tuple;
Py_INCREF(tuple);
}
}
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyBytes_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+ else
+ return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+ } else {
+ int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
+ #if CYTHON_PEP393_ENABLED
+ if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
+ return -1;
+ if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_LENGTH(s1) == 1) {
+ Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
+ Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #else
+ if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_SIZE(s1) == 1) {
+ Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
+ Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #endif
+ } else {
+ int result = PyUnicode_Compare(s1, s2);
+ if ((result == -1) && unlikely(PyErr_Occurred()))
+ return -1;
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
static PyObject *__Pyx_Generator_Close(PyObject *self);
static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static PyTypeObject *__pyx_GeneratorType = 0;
-#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
-#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
- PyObject *et, *ev, *tb;
- PyObject *value = NULL;
- __Pyx_ErrFetch(&et, &ev, &tb);
- if (!et) {
- Py_XDECREF(tb);
- Py_XDECREF(ev);
- Py_INCREF(Py_None);
- *pvalue = Py_None;
- return 0;
- }
- if (unlikely(et != PyExc_StopIteration) &&
- unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- if (likely(et == PyExc_StopIteration)) {
- if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
- if (!ev) {
- Py_INCREF(Py_None);
- ev = Py_None;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
- *pvalue = ev;
- return 0;
- }
- }
- PyErr_NormalizeException(&et, &ev, &tb);
- if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
-#if PY_VERSION_HEX >= 0x030300A0
- value = ((PyStopIterationObject *)ev)->value;
- Py_INCREF(value);
- Py_DECREF(ev);
-#else
- {
- PyObject* args = PyObject_GetAttrString(ev, "args");
- Py_DECREF(ev);
- if (likely(args)) {
- value = PyObject_GetItem(args, 0);
- Py_DECREF(args);
- }
- if (unlikely(!value)) {
- __Pyx_ErrRestore(NULL, NULL, NULL);
- Py_INCREF(Py_None);
- value = Py_None;
- }
- }
-#endif
- *pvalue = value;
- return 0;
-}
-#endif
static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
+{
PyObject *exc_type = self->exc_type;
PyObject *exc_value = self->exc_value;
PyObject *exc_traceback = self->exc_traceback;
Py_XDECREF(exc_traceback);
}
static CYTHON_INLINE
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
- if (unlikely(gen->is_running)) {
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
+{
+ PyObject *retval;
+ if (unlikely(self->is_running)) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return 1;
+ return NULL;
}
- return 0;
-}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
- PyObject *retval;
- assert(!self->is_running);
if (unlikely(self->resume_label == 0)) {
if (unlikely(value && value != Py_None)) {
PyErr_SetString(PyExc_TypeError,
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
- if (value) {
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Generators always return to their most recent caller, not
- * necessarily their creator. */
- if (self->exc_traceback) {
- PyThreadState *tstate = PyThreadState_GET();
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_XINCREF(tstate->frame);
- assert(f->f_back == NULL);
- f->f_back = tstate->frame;
- }
-#endif
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
- &self->exc_traceback);
- } else {
+ if (value)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
__Pyx_Generator_ExceptionClear(self);
- }
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
- if (retval) {
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
- &self->exc_traceback);
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Don't keep the reference to f_back any longer than necessary. It
- * may keep a chain of frames alive or it could create a reference
- * cycle. */
- if (self->exc_traceback) {
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_CLEAR(f->f_back);
- }
-#endif
- } else {
+ if (retval)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
__Pyx_Generator_ExceptionClear(self);
- }
return retval;
}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
- PyObject *ret;
- PyObject *val = NULL;
- __Pyx_Generator_Undelegate(gen);
- __Pyx_PyGen_FetchStopIterationValue(&val);
- ret = __Pyx_Generator_SendEx(gen, val);
- Py_XDECREF(val);
- return ret;
-}
-static PyObject *__Pyx_Generator_Next(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- ret = Py_TYPE(yf)->tp_iternext(yf);
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, Py_None);
-}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Send(yf, value);
- } else {
- if (value == Py_None)
- ret = PyIter_Next(yf);
- else
- ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
- }
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, value);
+static PyObject *__Pyx_Generator_Next(PyObject *self)
+{
+ return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
}
-static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
- PyObject *retval = NULL;
- int err = 0;
- if (__Pyx_Generator_CheckExact(yf)) {
- retval = __Pyx_Generator_Close(yf);
- if (!retval)
- return -1;
- } else {
- PyObject *meth;
- gen->is_running = 1;
- meth = PyObject_GetAttrString(yf, "close");
- if (unlikely(!meth)) {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_WriteUnraisable(yf);
- }
- PyErr_Clear();
- } else {
- retval = PyObject_CallFunction(meth, NULL);
- Py_DECREF(meth);
- if (!retval)
- err = -1;
- }
- gen->is_running = 0;
- }
- Py_XDECREF(retval);
- return err;
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
+{
+ return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
}
-static PyObject *__Pyx_Generator_Close(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject *retval, *raised_exception;
- PyObject *yf = gen->yieldfrom;
- int err = 0;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- Py_INCREF(yf);
- err = __Pyx_Generator_CloseIter(gen, yf);
- __Pyx_Generator_Undelegate(gen);
- Py_DECREF(yf);
- }
- if (err == 0)
+static PyObject *__Pyx_Generator_Close(PyObject *self)
+{
+ __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ PyObject *retval;
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(gen, NULL);
+ retval = __Pyx_Generator_SendEx(generator, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
- raised_exception = PyErr_Occurred();
- if (!raised_exception
- || raised_exception == PyExc_StopIteration
-#if PY_VERSION_HEX >= 0x02050000
- || raised_exception == PyExc_GeneratorExit
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
+#if PY_VERSION_HEX < 0x02050000
+ if (PyErr_ExceptionMatches(PyExc_StopIteration))
+#else
+ if (PyErr_ExceptionMatches(PyExc_StopIteration)
+ || PyErr_ExceptionMatches(PyExc_GeneratorExit))
#endif
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- if (raised_exception) PyErr_Clear(); /* ignore these errors */
+ PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
+{
+ __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
- PyObject *yf = gen->yieldfrom;
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- Py_INCREF(yf);
-#if PY_VERSION_HEX >= 0x02050000
- if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
- int err = __Pyx_Generator_CloseIter(gen, yf);
- Py_DECREF(yf);
- __Pyx_Generator_Undelegate(gen);
- if (err < 0)
- return __Pyx_Generator_SendEx(gen, NULL);
- goto throw_here;
- }
-#endif
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Throw(yf, args);
- } else {
- PyObject *meth = PyObject_GetAttrString(yf, "throw");
- if (unlikely(!meth)) {
- Py_DECREF(yf);
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- gen->is_running = 0;
- return NULL;
- }
- PyErr_Clear();
- __Pyx_Generator_Undelegate(gen);
- gen->is_running = 0;
- goto throw_here;
- }
- ret = PyObject_CallObject(meth, args);
- Py_DECREF(meth);
- }
- gen->is_running = 0;
- Py_DECREF(yf);
- if (!ret) {
- ret = __Pyx_Generator_FinishDelegation(gen);
- }
- return ret;
- }
-throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(gen, NULL);
+ return __Pyx_Generator_SendEx(generator, NULL);
}
-static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
+static int
+__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
+{
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
Py_VISIT(gen->closure);
Py_VISIT(gen->classobj);
- Py_VISIT(gen->yieldfrom);
Py_VISIT(gen->exc_type);
Py_VISIT(gen->exc_value);
Py_VISIT(gen->exc_traceback);
return 0;
}
-static int __Pyx_Generator_clear(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->yieldfrom);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
+static void
+__Pyx_Generator_dealloc(PyObject *self)
+{
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject_GC_UnTrack(gen);
if (gen->gi_weakreflist != NULL)
return; /* resurrected. :( */
}
PyObject_GC_UnTrack(self);
- __Pyx_Generator_clear(self);
+ Py_CLEAR(gen->closure);
+ Py_CLEAR(gen->classobj);
+ Py_CLEAR(gen->exc_type);
+ Py_CLEAR(gen->exc_value);
+ Py_CLEAR(gen->exc_traceback);
PyObject_GC_Del(gen);
}
-static void __Pyx_Generator_del(PyObject *self) {
+static void
+__Pyx_Generator_del(PyObject *self)
+{
PyObject *res;
PyObject *error_type, *error_value, *error_traceback;
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
_Py_NewReference(self);
self->ob_refcnt = refcnt;
}
-#if CYTHON_COMPILING_FOR_CPYTHON
assert(PyType_IS_GC(self->ob_type) &&
_Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
/* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
* we need to undo that. */
_Py_DEC_REFTOTAL;
-#endif
/* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
* chain, so no more to do there.
* If COUNT_ALLOCS, the original decref bumped tp_frees, and
* undone.
*/
#ifdef COUNT_ALLOCS
- --Py_TYPE(self)->tp_frees;
- --Py_TYPE(self)->tp_allocs;
+ --self->ob_type->tp_frees;
+ --self->ob_type->tp_allocs;
#endif
}
static PyMemberDef __pyx_Generator_memberlist[] = {
{(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
- T_BOOL,
-#else
- T_BYTE,
-#endif
+ T_INT,
offsetof(__pyx_GeneratorObject, is_running),
READONLY,
NULL},
{__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_GeneratorType_type = {
+static PyTypeObject __pyx_GeneratorType = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("generator"), /*tp_name*/
sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
- 0, /*tp_getattro*/
+ PyObject_GenericGetAttr, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
0, /*tp_clear*/
0, /*tp_richcompare*/
offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
+ PyObject_SelfIter, /*tp_iter*/
(iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
__pyx_Generator_methods, /*tp_methods*/
__pyx_Generator_memberlist, /*tp_members*/
0, /*tp_version_tag*/
#endif
};
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure) {
+static
+__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure)
+{
__pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
if (gen == NULL)
return NULL;
gen->body = body;
gen->is_running = 0;
gen->resume_label = 0;
gen->classobj = NULL;
- gen->yieldfrom = NULL;
gen->exc_type = NULL;
gen->exc_value = NULL;
gen->exc_traceback = NULL;
PyObject_GC_Track(gen);
return gen;
}
-static int __pyx_Generator_init(void) {
- __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
- __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
- if (PyType_Ready(&__pyx_GeneratorType_type)) {
- return -1;
- }
- __pyx_GeneratorType = &__pyx_GeneratorType_type;
- return 0;
+static int __pyx_Generator_init(void)
+{
+ return PyType_Ready(&__pyx_GeneratorType);
}
static int __Pyx_check_binary_version(void) {
return 0;
}
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
}
#endif
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
projects / python-pysam.git / commitdiff