-/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
+/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
};
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_9csamtools_PileupRead;
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
struct __pyx_obj_5pysam_9csamtools_IteratorRow;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_5pysam_9csamtools_Samfile;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
+struct __pyx_obj_5pysam_9csamtools_SNPCall;
+struct __pyx_obj_5pysam_9csamtools_AlignedRead;
+struct __pyx_obj_5pysam_9csamtools_Fastqfile;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
+struct __pyx_obj_5pysam_9csamtools_IndexedReads;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
struct __pyx_obj_5pysam_9csamtools_IteratorColumn;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
+struct __pyx_obj_5pysam_9csamtools_Samfile;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs;
struct __pyx_obj_5pysam_9csamtools_Fastafile;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
struct __pyx_obj_5pysam_9csamtools_PileupProxy;
-struct __pyx_obj_5pysam_9csamtools_IndexedReads;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
-struct __pyx_obj_5pysam_9csamtools_AlignedRead;
-struct __pyx_obj_5pysam_9csamtools_SNPCall;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
+struct __pyx_obj_5pysam_9csamtools_PileupRead;
+struct __pyx_obj_5pysam_9csamtools_FastqProxy;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
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
+/* "pysam/csamtools.pxd":414
* # Utility types
*
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
int seq_len;
};
-/* "pysam/csamtools.pxd":523
+/* "pysam/csamtools.pxd":554
* cdef char * getSequence( self )
* cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
int reopen;
};
-/* "pysam/csamtools.pyx":518
+/* "pysam/csamtools.pyx":644
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
uint32_t flag;
};
-/* "pysam/csamtools.pxd":455
- * cdef int n_pu
+/* "pysam/csamtools.pxd":495
+ * cdef uint32_t _is_tail
+ *
+ * cdef class IteratorRow: # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class PileupRead: # <<<<<<<<<<<<<<
- * cdef AlignedRead _alignment
- * cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_PileupRead {
+struct __pyx_obj_5pysam_9csamtools_IteratorRow {
PyObject_HEAD
- struct __pyx_obj_5pysam_9csamtools_AlignedRead *_alignment;
- int32_t _qpos;
- int _indel;
- int _level;
- uint32_t _is_del;
- uint32_t _is_head;
- uint32_t _is_tail;
};
-/* "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) )
+/* "pysam/csamtools.pxd":518
+ * cdef int cnext(self)
+ *
+ * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef int tid
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ int tid;
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *rowiter;
+};
+
+
+/* "pysam/csamtools.pyx":3467
+ * return retval, out_stderr, out_stdout
+ *
+ * cdef class SNPCall: # <<<<<<<<<<<<<<
+ * '''the results of a SNP call.'''
+ * cdef int _tid
+ */
+struct __pyx_obj_5pysam_9csamtools_SNPCall {
PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ int _tid;
+ int _pos;
+ char _reference_base;
+ char _genotype;
+ int _consensus_quality;
+ int _snp_quality;
+ int _rms_mapping_quality;
+ int _coverage;
};
-/* "pysam/csamtools.pxd":464
- * cdef uint32_t _is_tail
+/* "pysam/csamtools.pxd":446
+ * cdef int cnext(self)
*
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * pass
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
*
+ * # object that this AlignedRead represents
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow {
+struct __pyx_obj_5pysam_9csamtools_AlignedRead {
PyObject_HEAD
+ bam1_t *_delegate;
};
-/* "pysam/csamtools.pxd":467
- * pass
+/* "pysam/csamtools.pxd":438
+ * cdef kseq_t * _delegate
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam_iter_t iter # iterator state object
- * cdef bam1_t * b
+ * cdef class Fastqfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * cdef gzFile fastqfile
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
+struct __pyx_obj_5pysam_9csamtools_Fastqfile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtab;
+ char *_filename;
+ gzFile fastqfile;
+ kseq_t *entry;
+};
+
+
+/* "pysam/csamtools.pxd":523
+ * cdef IteratorRowRegion rowiter
+ *
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef int current_pos
+ */
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
+ struct __pyx_vtabstruct_5pysam_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.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( "(\d+)([MIDNSHP=X])" )
+/* "pysam/csamtools.pxd":570
+ * pass
*
+ * cdef class IndexedReads: # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
+struct __pyx_obj_5pysam_9csamtools_IndexedReads {
PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ PyObject *index;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":420
- * cdef bam1_t * _delegate
+/* "pysam/csamtools.pxd":511
+ * 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_5pysam_9csamtools_IteratorRowAll {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtab;
bam1_t *b;
- char *mode;
- int64_t start_offset;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":504
+/* "pysam/csamtools.pxd":535
* cdef int cnext(self)
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
};
-/* "pysam/csamtools.pxd":536
+/* "pysam/csamtools.pxd":562
+ * cdef reset( self, tid, start, end )
+ *
+ * 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;
+};
+
+
+/* "pysam/csamtools.pxd":451
+ * cdef bam1_t * _delegate
+ *
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
+ */
+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;
+ bam1_t *b;
+ char *mode;
+ int64_t start_offset;
+};
+
+
+/* "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( "(\d+)([MIDNSHP=X])" )
+ *
+ */
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_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":567
* cdef int truncate
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
};
-/* "pysam/csamtools.pxd":408
+/* "pysam/csamtools.pxd":428
* # Note: need to declare all C fields and methods here
* #
* cdef class Fastafile: # <<<<<<<<<<<<<<
};
-/* "pysam/csamtools.pxd":449
+/* "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":480
* cdef char * _getrname( self, int tid )
*
* cdef class PileupProxy: # <<<<<<<<<<<<<<
};
-/* "pysam/csamtools.pxd":539
- * pass
+/* "pysam/csamtools.pxd":486
+ * cdef int n_pu
*
- * cdef class IndexedReads: # <<<<<<<<<<<<<<
- * cdef Samfile samfile
- * cdef samfile_t * fp
+ * cdef class PileupRead: # <<<<<<<<<<<<<<
+ * cdef AlignedRead _alignment
+ * cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_IndexedReads {
+struct __pyx_obj_5pysam_9csamtools_PileupRead {
PyObject_HEAD
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- samfile_t *fp;
- PyObject *index;
- int owns_samfile;
-};
-
-
-/* "pysam/csamtools.pxd":480
- * cdef int cnext(self)
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef samfile_t * fp
- */
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAll {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtab;
- bam1_t *b;
- samfile_t *fp;
- int owns_samfile;
-};
-
-
-/* "pysam/csamtools.pxd":531
- * cdef reset( self, tid, start, end )
- *
- * 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;
-};
-
-
-/* "pysam/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;
- int tid;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *rowiter;
+ struct __pyx_obj_5pysam_9csamtools_AlignedRead *_alignment;
+ int32_t _qpos;
+ int _indel;
+ int _level;
+ uint32_t _is_del;
+ uint32_t _is_head;
+ uint32_t _is_tail;
};
-/* "pysam/csamtools.pxd":415
+/* "pysam/csamtools.pxd":435
* cdef char * _fetch( self, char * reference, int start, int end, int * length )
*
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ * cdef class FastqProxy: # <<<<<<<<<<<<<<
+ * cdef kseq_t * _delegate
*
- * # object that this AlignedRead represents
*/
-struct __pyx_obj_5pysam_9csamtools_AlignedRead {
+struct __pyx_obj_5pysam_9csamtools_FastqProxy {
PyObject_HEAD
- bam1_t *_delegate;
+ kseq_t *_delegate;
};
-/* "pysam/csamtools.pyx":3250
- * return retval, out_stderr, out_stdout
- *
- * cdef class SNPCall: # <<<<<<<<<<<<<<
- * '''the results of a SNP call.'''
- * cdef int _tid
- */
-struct __pyx_obj_5pysam_9csamtools_SNPCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- char _reference_base;
- char _genotype;
- int _consensus_quality;
- int _snp_quality;
- int _rms_mapping_quality;
- int _coverage;
-};
-
-
-/* "pysam/csamtools.pxd":492
- * cdef IteratorRowRegion rowiter
+/* "pysam/csamtools.pxd":498
+ * pass
*
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef int current_pos
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam_iter_t iter # iterator state object
+ * cdef bam1_t * b
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
+ bam_iter_t iter;
bam1_t *b;
- int current_pos;
+ int retval;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
samfile_t *fp;
- PyObject *positions;
int owns_samfile;
};
-/* "pysam/csamtools.pyx":545
+/* "pysam/csamtools.pyx":1921
+ * return ret
*
+ * cdef class IteratorColumn: # <<<<<<<<<<<<<<
+ * '''abstract base class for iterators over columns.
*
- * 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_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 *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
-/* "pysam/csamtools.pyx":1545
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
+/* "pysam/csamtools.pyx":2083
+ * 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_5pysam_9csamtools_IteratorColumnRegion {
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
-/* "pysam/csamtools.pyx":1466
+/* "pysam/csamtools.pyx":1597
*
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
-/* "pysam/csamtools.pyx":1771
- * return ret
+/* "pysam/csamtools.pyx":1792
+ * raise StopIteration
*
- * cdef class IteratorColumn: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over columns.
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
*
*/
-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_5pysam_9csamtools_IteratorRowSelection {
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
-/* "pysam/csamtools.pyx":1936
- * self.iterdata.seq = NULL
+/* "pysam/csamtools.pyx":382
+ * ## 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_5pysam_9csamtools_Fastafile {
+ char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
+
+
+/* "pysam/csamtools.pyx":546
+ * else: return None
+ *
+ * cdef class Fastqfile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile {
+ kseq_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *);
+};
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtabptr_5pysam_9csamtools_Fastqfile;
-/* "pysam/csamtools.pyx":1973
+/* "pysam/csamtools.pyx":2120
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
-/* "pysam/csamtools.pyx":1646
- * raise StopIteration
+/* "pysam/csamtools.pyx":671
*
- * 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_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);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
-/* "pysam/csamtools.pyx":375
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
+/* "pysam/csamtools.pyx":1681
+ * if self.owns_samfile: samclose( self.fp )
+ *
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int reopen = True)*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
- char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll {
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
/* Module declarations from 'pysam.csamtools' */
static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastafile = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_FastqProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastqfile = 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 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_makeFastqProxy(kseq_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 PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IOError;
+static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_OverflowError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_OSError;
static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_sorted;
static PyObject *__pyx_builtin_KeyError;
-static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_min;
static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_chr;
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_10FastqProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_4name___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_8sequence___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_7comment___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_7quality___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_9Fastqfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_4_open(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_6close(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_9Fastqfile_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_10__iter__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_12__next__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_14test(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* 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_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_15inferred_length___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 char __pyx_k_17[] = "start out of range (%i)";
static char __pyx_k_18[] = "end out of range (%i)";
static char __pyx_k_19[] = "%s:%i-%i";
-static char __pyx_k_24[] = "invalid file opening mode `%s`";
-static char __pyx_k_26[] = "-";
-static char __pyx_k_27[] = "http:";
-static char __pyx_k_28[] = "ftp:";
-static char __pyx_k_29[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
-static char __pyx_k_30[] = "unequal names and lengths of reference sequences";
-static char __pyx_k_31[] = "@SQ\tSN:%s\tLN:%s\n";
-static char __pyx_k_32[] = "file `%s` not found";
-static char __pyx_k_33[] = "could not open file (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_34[] = "file does not have valid header (mode='%s') - is it BAM format?";
-static char __pyx_k_35[] = "file does not have valid header (mode='%s') - is it SAM format?";
-static char __pyx_k_36[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_37[] = ".bai";
-static char __pyx_k_38[] = "error while opening index `%s` ";
-static char __pyx_k_41[] = "tid %i out of range 0<=tid<%i";
-static char __pyx_k_43[] = "[:-]";
-static char __pyx_k_45[] = "invalid reference `%s`";
-static char __pyx_k_46[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_48[] = "seek only available in bam files";
-static char __pyx_k_50[] = "seek no available in streams";
-static char __pyx_k_56[] = "fetch called on bamfile without index";
-static char __pyx_k_58[] = "callback functionality requires a region/reference";
-static char __pyx_k_60[] = "no index available for fetch";
-static char __pyx_k_62[] = "fetching by region is not available for sam files";
-static char __pyx_k_64[] = "callback not implemented yet";
-static char __pyx_k_66[] = "fetch called for samfile without header";
-static char __pyx_k_69[] = "read %s: is unpaired";
-static char __pyx_k_70[] = "mate %s: is unmapped";
-static char __pyx_k_71[] = "mate not found";
-static char __pyx_k_76[] = "counting functionality requires a region/reference";
-static char __pyx_k_79[] = "count for a region is not available for sam files";
-static char __pyx_k_82[] = "no index available for pileup";
-static char __pyx_k_85[] = "pileup of samfiles not implemented yet";
-static char __pyx_k_92[] = "Samfile.mapped only available in bam files";
-static char __pyx_k_94[] = "mapping information not recorded in index or index not available";
-static char __pyx_k_97[] = "Samfile.unmapped only available in bam files";
+static char __pyx_k_21[] = "No such file or directory: %s";
+static char __pyx_k_24[] = "name: %s\n";
+static char __pyx_k_25[] = "comment: %s\n";
+static char __pyx_k_26[] = "seq: %s\n";
+static char __pyx_k_27[] = "qual: %s\n";
+static char __pyx_k_28[] = "return value: %d\n";
+static char __pyx_k_32[] = "invalid file opening mode `%s`";
+static char __pyx_k_34[] = "-";
+static char __pyx_k_35[] = "http:";
+static char __pyx_k_36[] = "ftp:";
+static char __pyx_k_37[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
+static char __pyx_k_38[] = "unequal names and lengths of reference sequences";
+static char __pyx_k_39[] = "@SQ\tSN:%s\tLN:%s\n";
+static char __pyx_k_40[] = "file `%s` not found";
+static char __pyx_k_41[] = "could not open file (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_42[] = "file does not have valid header (mode='%s') - is it BAM format?";
+static char __pyx_k_43[] = "file does not have valid header (mode='%s') - is it SAM format?";
+static char __pyx_k_44[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_45[] = ".bai";
+static char __pyx_k_46[] = "error while opening index `%s` ";
+static char __pyx_k_49[] = "tid %i out of range 0<=tid<%i";
+static char __pyx_k_51[] = "[:-]";
+static char __pyx_k_53[] = "invalid reference `%s`";
+static char __pyx_k_54[] = "invalid coordinates: start (%i) > end (%i)";
+static char __pyx_k_56[] = "seek only available in bam files";
+static char __pyx_k_58[] = "seek no available in streams";
+static char __pyx_k_64[] = "fetch called on bamfile without index";
+static char __pyx_k_66[] = "callback functionality requires a region/reference";
+static char __pyx_k_68[] = "no index available for fetch";
+static char __pyx_k_70[] = "fetching by region is not available for sam files";
+static char __pyx_k_72[] = "callback not implemented yet";
+static char __pyx_k_74[] = "fetch called for samfile without header";
+static char __pyx_k_77[] = "read %s: is unpaired";
+static char __pyx_k_78[] = "mate %s: is unmapped";
+static char __pyx_k_79[] = "mate not found";
+static char __pyx_k_84[] = "counting functionality requires a region/reference";
+static char __pyx_k_87[] = "count for a region is not available for sam files";
+static char __pyx_k_90[] = "no index available for pileup";
+static char __pyx_k_93[] = "pileup of samfiles not implemented yet";
static char __pyx_k__A[] = "A";
static char __pyx_k__B[] = "B";
static char __pyx_k__C[] = "C";
static char __pyx_k__r[] = "r";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
-static char __pyx_k_102[] = "@";
-static char __pyx_k_104[] = "header line without '@': '%s'";
-static char __pyx_k_106[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_107[] = ":";
-static char __pyx_k_108[] = "malformatted header: no ':' in field";
-static char __pyx_k_111[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_112[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_113[] = "@%s";
-static char __pyx_k_114[] = "%s:%s";
-static char __pyx_k_115[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_117[] = "incomplete sequence information in '%s'";
-static char __pyx_k_120[] = "can not iterate over samfile without header";
-static char __pyx_k_123[] = "no index available for iteration";
-static char __pyx_k_129[] = "can only use this iterator on bam files";
-static char __pyx_k_130[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_131[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_133[] = "error during iteration";
-static char __pyx_k_136[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_139[] = "%i%c";
-static char __pyx_k_140[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_141[] = "%c";
-static char __pyx_k_142[] = "<";
-static char __pyx_k_144[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_145[] = "2sccI%i%s";
-static char __pyx_k_149[] = "2sc%is";
-static char __pyx_k_151[] = "create_string_buffer";
-static char __pyx_k_152[] = "tag '%s' not present";
-static char __pyx_k_153[] = "unknown auxilliary type '%s'";
-static char __pyx_k_154[] = "Contig index";
-static char __pyx_k_155[] = "Mapped position on contig";
-static char __pyx_k_156[] = "Contig index for mate pair";
-static char __pyx_k_157[] = "Position of mate pair";
-static char __pyx_k_158[] = "Insert size";
-static char __pyx_k_159[] = "Binary flag";
-static char __pyx_k_160[] = "Count of cigar entries";
-static char __pyx_k_161[] = "Cigar entries";
-static char __pyx_k_162[] = "Mapping quality";
-static char __pyx_k_163[] = "Bam index bin number";
-static char __pyx_k_164[] = "Length of query name";
-static char __pyx_k_165[] = "Query name";
-static char __pyx_k_166[] = "Length of query sequence";
-static char __pyx_k_167[] = "Query sequence";
-static char __pyx_k_168[] = "Quality scores";
-static char __pyx_k_169[] = "Length of auxilary data";
-static char __pyx_k_170[] = "Maximum data length";
-static char __pyx_k_171[] = "Current data length";
-static char __pyx_k_172[] = "%-30s %-10s= %s";
-static char __pyx_k_173[] = "(";
-static char __pyx_k_174[] = ")";
-static char __pyx_k_175[] = "This class cannot be instantiated from Python";
-static char __pyx_k_177[] = "PileupProxy accessed after iterator finished";
-static char __pyx_k_181[] = "No such file or directory: '%s'";
-static char __pyx_k_182[] = "-o";
-static char __pyx_k_183[] = "option -o is forbidden in samtools view";
-static char __pyx_k_189[] = "can only IndexReads on bam files";
-static char __pyx_k_190[] = "read %s not found";
-static char __pyx_k_191[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_192[] = "the query name (None if not present)";
-static char __pyx_k_193[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of tuples of (operation, length). \n The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 |\n +-----+--------------+-----+\n |S |BAM_CSOFT_CLIP|4 |\n +-----+--------------+-----+\n |H |BAM_CHARD_CLIP|5 |\n +-----+--------------+-----+\n |P |BAM_CPAD |6 |\n +-----+--------------+-----+\n |= |BAM_CEQUAL |7 |\n +-----+--------------+-----+\n |X |BAM_CDIFF |8 |\n +-----+--------------+-----+\n\n .. note::\n The output is a list of (operation, length) tuples, such as\n ``[ (0, 30) ]``.\n This is different from the SAM specification and the\n the :meth:`cigarstring` property, which uses a\n (length,operation order, for example: ``30M``.\n\n ";
-static char __pyx_k_194[] = "the :term:`cigar` alignment as a string.\n \n The cigar string is a string of alternating integers\n and characters denoting the length and the type of\n an operation.\n\n .. note::\n The order length,operation is specified in the\n SAM format. It is different from the order of\n the :meth:`cigar` property.\n\n Returns the empty string if not present.\n ";
-static char __pyx_k_195[] = "read sequence bases, including :term:`soft clipped` bases (None if not present).\n\n 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.";
-static char __pyx_k_196[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present).\n\n 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.";
-static char __pyx_k_197[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
-static char __pyx_k_198[] = "aligned query sequence quality values (None if not present). This property is read-only.\n\n In Python 3, this property is of type bytes.";
-static char __pyx_k_199[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_200[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_201[] = "Length of the aligned query sequence";
-static char __pyx_k_202[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n ";
-static char __pyx_k_203[] = "properties flag";
-static char __pyx_k_204[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
-static char __pyx_k_205[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
-static char __pyx_k_206[] = "0-based leftmost coordinate";
-static char __pyx_k_207[] = "properties bin";
-static char __pyx_k_208[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_209[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available.";
-static char __pyx_k_210[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
-static char __pyx_k_211[] = "mapping quality";
-static char __pyx_k_212[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
-static char __pyx_k_213[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_214[] = "the position of the mate\n deprecated, use PNEXT instead.";
-static char __pyx_k_215[] = "the position of the mate";
-static char __pyx_k_216[] = "the insert size\n deprecated: use tlen instead";
-static char __pyx_k_217[] = "the insert size";
-static char __pyx_k_218[] = "true if read is paired in sequencing";
-static char __pyx_k_219[] = "true if read is mapped in a proper pair";
-static char __pyx_k_220[] = "true if read itself is unmapped";
-static char __pyx_k_221[] = "true if the mate is unmapped";
-static char __pyx_k_222[] = "true if read is mapped to reverse strand";
-static char __pyx_k_223[] = "true is read is mapped to reverse strand";
-static char __pyx_k_224[] = "true if this is read1";
-static char __pyx_k_225[] = "true if this is read2";
-static char __pyx_k_226[] = "true if not primary alignment";
-static char __pyx_k_227[] = "true if QC failure";
-static char __pyx_k_228[] = "true if optical or PCR duplicate";
-static char __pyx_k_229[] = "a list of reference positions that this read aligns to.";
-static char __pyx_k_230[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
-static char __pyx_k_231[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_232[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_233[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n ";
-static char __pyx_k_234[] = "total number of mapped reads in file.\n ";
-static char __pyx_k_235[] = "total number of unmapped reads in file.\n ";
-static char __pyx_k_236[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_237[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n ";
-static char __pyx_k_238[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_239[] = "number of reads mapping to this column.";
-static char __pyx_k_240[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_241[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_242[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_243[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_244[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_245[] = "current sequence length.";
-static char __pyx_k_246[] = "nucleotide position of SNP.";
-static char __pyx_k_247[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_248[] = "the genotype called.";
-static char __pyx_k_249[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_250[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_251[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_252[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_253[] = "getfilesystemencoding";
-static char __pyx_k_254[] = "MIDNSHP=X";
-static char __pyx_k_255[] = "(\\d+)([MIDNSHP=X])";
-static char __pyx_k_257[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_260[] = "/home/andreas/devel/pysam/pysam/csamtools.pyx";
-static char __pyx_k_261[] = "PileupColumn.__str__";
-static char __pyx_k_262[] = "pysam.csamtools";
-static char __pyx_k_263[] = "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_266[] = "StderrStore.__init__";
-static char __pyx_k_269[] = "StderrStore.readAndRelease";
-static char __pyx_k_272[] = "StderrStore.release";
-static char __pyx_k_275[] = "StderrStore.__del__";
-static char __pyx_k_276[] = "\n stderr is captured.\n ";
-static char __pyx_k_279[] = "StderrStoreWindows.__init__";
-static char __pyx_k_282[] = "StderrStoreWindows.readAndRelease";
-static char __pyx_k_285[] = "StderrStoreWindows.release";
-static char __pyx_k_286[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_295[] = "Outs.__init__";
-static char __pyx_k_298[] = "Outs.setdevice";
-static char __pyx_k_301[] = "Outs.setfile";
-static char __pyx_k_304[] = "Outs.setfd";
-static char __pyx_k_307[] = "Outs.restore";
-static char __pyx_k_308[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+static char __pyx_k_100[] = "Samfile.mapped only available in bam files";
+static char __pyx_k_102[] = "mapping information not recorded in index or index not available";
+static char __pyx_k_105[] = "Samfile.unmapped only available in bam files";
+static char __pyx_k_110[] = "@";
+static char __pyx_k_112[] = "header line without '@': '%s'";
+static char __pyx_k_114[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_115[] = ":";
+static char __pyx_k_116[] = "malformatted header: no ':' in field";
+static char __pyx_k_119[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_120[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_121[] = "@%s";
+static char __pyx_k_122[] = "%s:%s";
+static char __pyx_k_123[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_125[] = "incomplete sequence information in '%s'";
+static char __pyx_k_128[] = "can not iterate over samfile without header";
+static char __pyx_k_131[] = "no index available for iteration";
+static char __pyx_k_137[] = "can only use this iterator on bam files";
+static char __pyx_k_138[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_139[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_141[] = "error during iteration";
+static char __pyx_k_144[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_147[] = "%i%c";
+static char __pyx_k_148[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_149[] = "%c";
+static char __pyx_k_150[] = "<";
+static char __pyx_k_152[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_153[] = "2sccI%i%s";
+static char __pyx_k_157[] = "2sc%is";
+static char __pyx_k_159[] = "create_string_buffer";
+static char __pyx_k_160[] = "tag '%s' not present";
+static char __pyx_k_161[] = "unknown auxilliary type '%s'";
+static char __pyx_k_162[] = "Contig index";
+static char __pyx_k_163[] = "Mapped position on contig";
+static char __pyx_k_164[] = "Contig index for mate pair";
+static char __pyx_k_165[] = "Position of mate pair";
+static char __pyx_k_166[] = "Insert size";
+static char __pyx_k_167[] = "Binary flag";
+static char __pyx_k_168[] = "Count of cigar entries";
+static char __pyx_k_169[] = "Cigar entries";
+static char __pyx_k_170[] = "Mapping quality";
+static char __pyx_k_171[] = "Bam index bin number";
+static char __pyx_k_172[] = "Length of query name";
+static char __pyx_k_173[] = "Query name";
+static char __pyx_k_174[] = "Length of query sequence";
+static char __pyx_k_175[] = "Query sequence";
+static char __pyx_k_176[] = "Quality scores";
+static char __pyx_k_177[] = "Length of auxilary data";
+static char __pyx_k_178[] = "Maximum data length";
+static char __pyx_k_179[] = "Current data length";
+static char __pyx_k_180[] = "%-30s %-10s= %s";
+static char __pyx_k_181[] = "(";
+static char __pyx_k_182[] = ")";
+static char __pyx_k_183[] = "This class cannot be instantiated from Python";
+static char __pyx_k_185[] = "PileupProxy accessed after iterator finished";
+static char __pyx_k_189[] = "No such file or directory: '%s'";
+static char __pyx_k_190[] = "-o";
+static char __pyx_k_191[] = "option -o is forbidden in samtools view";
+static char __pyx_k_197[] = "can only IndexReads on bam files";
+static char __pyx_k_198[] = "read %s not found";
+static char __pyx_k_199[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_200[] = "the query name (None if not present)";
+static char __pyx_k_201[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of tuples of (operation, length). \n The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 |\n +-----+--------------+-----+\n |S |BAM_CSOFT_CLIP|4 |\n +-----+--------------+-----+\n |H |BAM_CHARD_CLIP|5 |\n +-----+--------------+-----+\n |P |BAM_CPAD |6 |\n +-----+--------------+-----+\n |= |BAM_CEQUAL |7 |\n +-----+--------------+-----+\n |X |BAM_CDIFF |8 |\n +-----+--------------+-----+\n\n .. note::\n The output is a list of (operation, length) tuples, such as\n ``[ (0, 30) ]``.\n This is different from the SAM specification and the\n the :meth:`cigarstring` property, which uses a\n (length,operation order, for example: ``30M``.\n\n ";
+static char __pyx_k_202[] = "the :term:`cigar` alignment as a string.\n \n The cigar string is a string of alternating integers\n and characters denoting the length and the type of\n an operation.\n\n .. note::\n The order length,operation is specified in the\n SAM format. It is different from the order of\n the :meth:`cigar` property.\n\n Returns the empty string if not present.\n ";
+static char __pyx_k_203[] = "read sequence bases, including :term:`soft clipped` bases \n (None if not present).\n\n In Python 3, this property is of type bytes and assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n Note that assigning to seq will invalidate any quality scores.\n Thus, to in-place edit the sequence and quality scores, copies of\n the quality scores need to be taken. Consider trimming for example::\n\n q = read.qual\n read.seq = read.seq[5:10]\n read.qual = q[5:10]\n\n ";
+static char __pyx_k_204[] = "read sequence base qualities, including :term:`soft\n clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n Note that to set quality scores the sequence has to be set\n previously as this will determine the permitted length of\n the quality score array.\n\n This method raises a ValueError if the length of the \n quality scores and the sequence are not the same.\n ";
+static char __pyx_k_205[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
+static char __pyx_k_206[] = "aligned query sequence quality values (None if not present). This property is read-only.\n\n In Python 3, this property is of type bytes.";
+static char __pyx_k_207[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_208[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_209[] = "Length of the aligned query sequence";
+static char __pyx_k_210[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n ";
+static char __pyx_k_211[] = "properties flag";
+static char __pyx_k_212[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
+static char __pyx_k_213[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
+static char __pyx_k_214[] = "0-based leftmost coordinate";
+static char __pyx_k_215[] = "properties bin";
+static char __pyx_k_216[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_217[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available.";
+static char __pyx_k_218[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
+static char __pyx_k_219[] = "mapping quality";
+static char __pyx_k_220[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
+static char __pyx_k_221[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_222[] = "the position of the mate\n deprecated, use PNEXT instead.";
+static char __pyx_k_223[] = "the position of the mate";
+static char __pyx_k_224[] = "the insert size\n deprecated: use tlen instead";
+static char __pyx_k_225[] = "the insert size";
+static char __pyx_k_226[] = "true if read is paired in sequencing";
+static char __pyx_k_227[] = "true if read is mapped in a proper pair";
+static char __pyx_k_228[] = "true if read itself is unmapped";
+static char __pyx_k_229[] = "true if the mate is unmapped";
+static char __pyx_k_230[] = "true if read is mapped to reverse strand";
+static char __pyx_k_231[] = "true is read is mapped to reverse strand";
+static char __pyx_k_232[] = "true if this is read1";
+static char __pyx_k_233[] = "true if this is read2";
+static char __pyx_k_234[] = "true if not primary alignment";
+static char __pyx_k_235[] = "true if QC failure";
+static char __pyx_k_236[] = "true if optical or PCR duplicate";
+static char __pyx_k_237[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_238[] = "inferred read length from CIGAR string.\n\n Returns 0 if CIGAR string is not present.\n ";
+static char __pyx_k_239[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
+static char __pyx_k_240[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_241[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_242[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n ";
+static char __pyx_k_243[] = "total number of mapped reads in file.\n ";
+static char __pyx_k_244[] = "total number of unmapped reads in file.\n ";
+static char __pyx_k_245[] = "full contents of the :term:`sam file` header as a string.";
+static char __pyx_k_246[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n ";
+static char __pyx_k_247[] = "the chromosome ID as is defined in the header";
+static char __pyx_k_248[] = "number of reads mapping to this column.";
+static char __pyx_k_249[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
+static char __pyx_k_250[] = "a :class:`pysam.AlignedRead` object of the aligned read";
+static char __pyx_k_251[] = "position of the read base at the pileup site, 0-based";
+static char __pyx_k_252[] = "indel length; 0 for no indel, positive for ins and negative for del";
+static char __pyx_k_253[] = "1 iff the base on the padded read is a deletion";
+static char __pyx_k_254[] = "current sequence length.";
+static char __pyx_k_255[] = "nucleotide position of SNP.";
+static char __pyx_k_256[] = "reference base at pos. ``N`` if no reference sequence supplied.";
+static char __pyx_k_257[] = "the genotype called.";
+static char __pyx_k_258[] = "the genotype quality (Phred-scaled).";
+static char __pyx_k_259[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
+static char __pyx_k_260[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
+static char __pyx_k_261[] = "coverage or read depth - the number of reads involved in the call.";
+static char __pyx_k_262[] = "getfilesystemencoding";
+static char __pyx_k_263[] = "MIDNSHP=X";
+static char __pyx_k_264[] = "(\\d+)([MIDNSHP=X])";
+static char __pyx_k_266[] = "=ACMGRSVTWYHKDBN";
+static char __pyx_k_269[] = "/home/andreas/devel/pysam/pysam/csamtools.pyx";
+static char __pyx_k_270[] = "PileupColumn.__str__";
+static char __pyx_k_271[] = "pysam.csamtools";
+static char __pyx_k_272[] = "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_275[] = "StderrStore.__init__";
+static char __pyx_k_278[] = "StderrStore.readAndRelease";
+static char __pyx_k_281[] = "StderrStore.release";
+static char __pyx_k_284[] = "StderrStore.__del__";
+static char __pyx_k_285[] = "\n stderr is captured.\n ";
+static char __pyx_k_288[] = "StderrStoreWindows.__init__";
+static char __pyx_k_291[] = "StderrStoreWindows.readAndRelease";
+static char __pyx_k_294[] = "StderrStoreWindows.release";
+static char __pyx_k_295[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_304[] = "Outs.__init__";
+static char __pyx_k_307[] = "Outs.setdevice";
+static char __pyx_k_310[] = "Outs.setfile";
+static char __pyx_k_313[] = "Outs.setfd";
+static char __pyx_k_316[] = "Outs.restore";
+static char __pyx_k_317[] = "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__truncate[] = "truncate";
static char __pyx_k__warnings[] = "warnings";
static char __pyx_k__Fastafile[] = "Fastafile";
+static char __pyx_k__Fastqfile[] = "Fastqfile";
static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k____enter__[] = "__enter__";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
static PyObject *__pyx_kp_u_1;
static PyObject *__pyx_kp_s_10;
+static PyObject *__pyx_kp_s_100;
static PyObject *__pyx_kp_s_102;
-static PyObject *__pyx_kp_s_104;
-static PyObject *__pyx_kp_s_106;
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{&__pyx_kp_s_152, __pyx_k_152, sizeof(__pyx_k_152), 0, 0, 1, 0},
{&__pyx_kp_s_153, __pyx_k_153, sizeof(__pyx_k_153), 0, 0, 1, 0},
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{&__pyx_kp_s_157, __pyx_k_157, sizeof(__pyx_k_157), 0, 0, 1, 0},
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{&__pyx_kp_b_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 0, 0},
{&__pyx_kp_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 0},
{&__pyx_kp_s_160, __pyx_k_160, sizeof(__pyx_k_160), 0, 0, 1, 0},
{&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0},
{&__pyx_kp_s_174, __pyx_k_174, sizeof(__pyx_k_174), 0, 0, 1, 0},
{&__pyx_kp_s_175, __pyx_k_175, sizeof(__pyx_k_175), 0, 0, 1, 0},
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{&__pyx_kp_s_177, __pyx_k_177, sizeof(__pyx_k_177), 0, 0, 1, 0},
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{&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
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{&__pyx_kp_s_181, __pyx_k_181, sizeof(__pyx_k_181), 0, 0, 1, 0},
{&__pyx_kp_s_182, __pyx_k_182, sizeof(__pyx_k_182), 0, 0, 1, 0},
{&__pyx_kp_s_183, __pyx_k_183, sizeof(__pyx_k_183), 0, 0, 1, 0},
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{&__pyx_kp_s_189, __pyx_k_189, sizeof(__pyx_k_189), 0, 0, 1, 0},
{&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
{&__pyx_kp_s_190, __pyx_k_190, sizeof(__pyx_k_190), 0, 0, 1, 0},
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{&__pyx_n_s_275, __pyx_k_275, sizeof(__pyx_k_275), 0, 0, 1, 1},
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{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
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{&__pyx_n_s_304, __pyx_k_304, sizeof(__pyx_k_304), 0, 0, 1, 1},
{&__pyx_n_s_307, __pyx_k_307, sizeof(__pyx_k_307), 0, 0, 1, 1},
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{&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
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+ {&__pyx_kp_s_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 1, 0},
{&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0},
+ {&__pyx_kp_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 0},
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{&__pyx_kp_s_41, __pyx_k_41, sizeof(__pyx_k_41), 0, 0, 1, 0},
+ {&__pyx_kp_s_42, __pyx_k_42, sizeof(__pyx_k_42), 0, 0, 1, 0},
{&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0},
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+ {&__pyx_kp_s_44, __pyx_k_44, sizeof(__pyx_k_44), 0, 0, 1, 0},
+ {&__pyx_kp_b_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 0, 0},
{&__pyx_kp_s_46, __pyx_k_46, sizeof(__pyx_k_46), 0, 0, 1, 0},
- {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0},
+ {&__pyx_kp_s_49, __pyx_k_49, sizeof(__pyx_k_49), 0, 0, 1, 0},
{&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0},
- {&__pyx_kp_s_50, __pyx_k_50, sizeof(__pyx_k_50), 0, 0, 1, 0},
+ {&__pyx_kp_s_51, __pyx_k_51, sizeof(__pyx_k_51), 0, 0, 1, 0},
+ {&__pyx_kp_s_53, __pyx_k_53, sizeof(__pyx_k_53), 0, 0, 1, 0},
+ {&__pyx_kp_s_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 0},
{&__pyx_kp_s_56, __pyx_k_56, sizeof(__pyx_k_56), 0, 0, 1, 0},
{&__pyx_kp_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 0},
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
- {&__pyx_kp_s_60, __pyx_k_60, sizeof(__pyx_k_60), 0, 0, 1, 0},
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{&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0},
{&__pyx_kp_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 0},
- {&__pyx_kp_s_69, __pyx_k_69, sizeof(__pyx_k_69), 0, 0, 1, 0},
+ {&__pyx_kp_s_68, __pyx_k_68, sizeof(__pyx_k_68), 0, 0, 1, 0},
{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
{&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0},
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- {&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0},
+ {&__pyx_kp_s_72, __pyx_k_72, sizeof(__pyx_k_72), 0, 0, 1, 0},
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+ {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0},
+ {&__pyx_kp_s_78, __pyx_k_78, sizeof(__pyx_k_78), 0, 0, 1, 0},
{&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0},
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- {&__pyx_kp_s_85, __pyx_k_85, sizeof(__pyx_k_85), 0, 0, 1, 0},
+ {&__pyx_kp_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 0},
+ {&__pyx_kp_s_87, __pyx_k_87, sizeof(__pyx_k_87), 0, 0, 1, 0},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
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- {&__pyx_kp_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 0},
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+ {&__pyx_kp_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 0},
{&__pyx_kp_s__2scB, __pyx_k__2scB, sizeof(__pyx_k__2scB), 0, 0, 1, 0},
{&__pyx_kp_s__2scH, __pyx_k__2scH, sizeof(__pyx_k__2scH), 0, 0, 1, 0},
{&__pyx_kp_s__2scI, __pyx_k__2scI, sizeof(__pyx_k__2scI), 0, 0, 1, 0},
{&__pyx_n_s__F, __pyx_k__F, sizeof(__pyx_k__F), 0, 0, 1, 1},
{&__pyx_n_s__FO, __pyx_k__FO, sizeof(__pyx_k__FO), 0, 0, 1, 1},
{&__pyx_n_s__Fastafile, __pyx_k__Fastafile, sizeof(__pyx_k__Fastafile), 0, 0, 1, 1},
+ {&__pyx_n_s__Fastqfile, __pyx_k__Fastqfile, sizeof(__pyx_k__Fastqfile), 0, 0, 1, 1},
{&__pyx_n_s__GO, __pyx_k__GO, sizeof(__pyx_k__GO), 0, 0, 1, 1},
{&__pyx_n_s__H, __pyx_k__H, sizeof(__pyx_k__H), 0, 0, 1, 1},
{&__pyx_n_s__HD, __pyx_k__HD, sizeof(__pyx_k__HD), 0, 0, 1, 1},
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static int __Pyx_InitCachedBuiltins(void) {
- __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_ord = __Pyx_GetName(__pyx_b, __pyx_n_s__ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_sorted = __Pyx_GetName(__pyx_b, __pyx_n_s__sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_min = __Pyx_GetName(__pyx_b, __pyx_n_s__min); if (!__pyx_builtin_min) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_max = __Pyx_GetName(__pyx_b, __pyx_n_s__max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_chr = __Pyx_GetName(__pyx_b, __pyx_n_s__chr); if (!__pyx_builtin_chr) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_UnicodeDecodeError = __Pyx_GetName(__pyx_b, __pyx_n_s__UnicodeDecodeError); if (!__pyx_builtin_UnicodeDecodeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __Pyx_GOTREF(__pyx_k_tuple_59);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));
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- __Pyx_GOTREF(__pyx_k_tuple_61);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
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- __Pyx_GOTREF(__pyx_k_tuple_63);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
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+ __Pyx_GOTREF(__pyx_k_tuple_71);
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- __Pyx_GOTREF(__pyx_k_tuple_65);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65));
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- __Pyx_GOTREF(__pyx_k_tuple_67);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67));
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- __Pyx_GOTREF(__pyx_k_tuple_68);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));
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- __Pyx_GOTREF(__pyx_k_tuple_72);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
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- __Pyx_GOTREF(__pyx_k_tuple_74);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74));
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+ __Pyx_GOTREF(__pyx_k_tuple_82);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_82));
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- __Pyx_GOTREF(__pyx_k_tuple_75);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
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- __Pyx_GOTREF(__pyx_k_tuple_77);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_84));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_91));
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* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_93));
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* def __get__(self):
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
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* def __get__(self):
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* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
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* def __get__(self):
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_100));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_101));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_105));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_116));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_119));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_125));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_126));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_127));
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__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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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_5pysam_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __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__;
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __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 = 671; __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 = 3029; __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 = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3246; __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 = 3246; __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 = 3081; __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 = 3081; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3298; __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 = 3298; __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 = 1446; __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 = 1446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1572; __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 = 1572; __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 = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __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 = 1597; __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__;
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __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 = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __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 = 1597; __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 = 1545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1545; __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 = 1681; __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__;
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1545; __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 = 1545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1681; __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 = 1681; __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 = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __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 = 1745; __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__;
}
}
#endif
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __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 = 1646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1646; __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 = 1792; __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__;
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1646; __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 = 1646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __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 = 1792; __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.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 = 1771; __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 = 1771; __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 = 1771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1921; __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 = 1921; __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 = 1921; __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 = 1936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
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/* "pysam/csamtools.pyx":1
projects / python-pysam.git / commitdiff