[med-svn] [python-pysam] 03/05: Imported Upstream version 0.7.7
Charles Plessy
plessy at moszumanska.debian.org
Sat Apr 19 02:48:44 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository python-pysam.
commit a757e53aa364a0816cbebb22c43c9918f08522f8
Author: Charles Plessy <plessy at debian.org>
Date: Sat Apr 19 11:42:00 2014 +0900
Imported Upstream version 0.7.7
---
PKG-INFO | 2 +-
doc/release.rst | 6 +
pysam.egg-info/PKG-INFO | 2 +-
pysam/TabProxies.c | 60 +-
pysam/csamtools.c | 13364 ++++++++++++++++++++++++++--------------------
pysam/csamtools.pxd | 12 +-
pysam/csamtools.pyx | 125 +-
pysam/ctabix.c | 5261 +++++++++---------
pysam/ctabix.pxd | 63 +-
pysam/ctabix.pyx | 262 +-
pysam/cvcf.c | 455 +-
pysam/tabix_util.c | 2 +
pysam/tabix_util.h | 7 +
pysam/version.py | 2 +-
tests/Makefile | 5 +-
tests/pysam_test.py | 61 +-
tests/tabix_test.py | 167 +-
17 files changed, 10690 insertions(+), 9166 deletions(-)
diff --git a/PKG-INFO b/PKG-INFO
index dbb2aed..663796e 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.6
+Version: 0.7.7
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/doc/release.rst b/doc/release.rst
index 3413c1f..062ab52 100644
--- a/doc/release.rst
+++ b/doc/release.rst
@@ -2,6 +2,12 @@
Release notes
=============
+Release 0.7.7
+=============
+
+ * added Fastafile.references, .nreferences and .lengths
+ * tabix_iterator now uses kseq.h for python 2.7
+
Release 0.7.6
=============
diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO
index dbb2aed..663796e 100644
--- a/pysam.egg-info/PKG-INFO
+++ b/pysam.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.6
+Version: 0.7.7
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/pysam/TabProxies.c b/pysam/TabProxies.c
index 099e19e..c1ab8fe 100644
--- a/pysam/TabProxies.c
+++ b/pysam/TabProxies.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
+/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -341,8 +341,8 @@ static const char *__pyx_f[] = {
/*--- Type declarations ---*/
struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_BedProxy;
struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
/* "pysam/TabProxies.pxd":41
@@ -377,6 +377,20 @@ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
};
+/* "pysam/TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
+};
+
+
/* "pysam/TabProxies.pxd":72
* pass
*
@@ -393,20 +407,6 @@ struct __pyx_obj_5pysam_10TabProxies_BedProxy {
};
-/* "pysam/TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
-};
-
-
/* "pysam/TabProxies.pxd":83
* cdef update( self, char * buffer, size_t nbytes )
*
@@ -454,20 +454,6 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
-/* "pysam/TabProxies.pyx":590
- * return f( self.fields[idx] )
- *
- * cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
- * '''Proxy class for access to Bed fields.
- *
- */
-
-struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
- struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
-};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
-
-
/* "pysam/TabProxies.pyx":656
* TupleProxy._setindex(self, idx, str(value) )
*
@@ -495,6 +481,20 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
+
+
+/* "pysam/TabProxies.pyx":590
+ * return f( self.fields[idx] )
+ *
+ * cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
+ * '''Proxy class for access to Bed fields.
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
diff --git a/pysam/csamtools.c b/pysam/csamtools.c
index 66c8778..5eff100 100644
--- a/pysam/csamtools.c
+++ b/pysam/csamtools.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
+/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -347,25 +347,28 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
+struct __pyx_obj_5pysam_9csamtools_PileupRead;
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_IteratorRow;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
+struct __pyx_obj_5pysam_9csamtools_IndexedReads;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr;
struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_5pysam_9csamtools_Fastqfile;
+struct __pyx_obj_5pysam_9csamtools_FastqProxy;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs;
struct __pyx_obj_5pysam_9csamtools_Fastafile;
+struct __pyx_obj_5pysam_9csamtools_AlignedRead;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
+struct __pyx_obj_5pysam_9csamtools_Samfile;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
struct __pyx_obj_5pysam_9csamtools_PileupProxy;
-struct __pyx_obj_5pysam_9csamtools_PileupRead;
-struct __pyx_obj_5pysam_9csamtools_FastqProxy;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
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;
@@ -388,7 +391,7 @@ struct __pyx_t_5pysam_9csamtools___iterdata {
int seq_len;
};
-/* "pysam/csamtools.pxd":554
+/* "pysam/csamtools.pxd":552
* cdef char * getSequence( self )
* cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
@@ -400,7 +403,7 @@ struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData {
int reopen;
};
-/* "pysam/csamtools.pyx":644
+/* "pysam/csamtools.pyx":657
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
@@ -413,34 +416,26 @@ struct __pyx_t_5pysam_9csamtools_MateData {
uint32_t flag;
};
-/* "pysam/csamtools.pxd":495
- * cdef uint32_t _is_tail
- *
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * pass
+/* "pysam/csamtools.pxd":484
+ * cdef int n_pu
*
+ * cdef class PileupRead: # <<<<<<<<<<<<<<
+ * cdef AlignedRead _alignment
+ * cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow {
+struct __pyx_obj_5pysam_9csamtools_PileupRead {
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.pxd":518
- * 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;
-};
-
-
-/* "pysam/csamtools.pyx":3467
+/* "pysam/csamtools.pyx":3474
* return retval, out_stderr, out_stdout
*
* cdef class SNPCall: # <<<<<<<<<<<<<<
@@ -460,54 +455,63 @@ struct __pyx_obj_5pysam_9csamtools_SNPCall {
};
-/* "pysam/csamtools.pxd":446
+/* "pysam/csamtools.pxd":533
* cdef int cnext(self)
*
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ * cdef class IteratorColumn: # <<<<<<<<<<<<<<
*
- * # object that this AlignedRead represents
+ * # result of the last plbuf_push
*/
-struct __pyx_obj_5pysam_9csamtools_AlignedRead {
+struct __pyx_obj_5pysam_9csamtools_IteratorColumn {
PyObject_HEAD
- bam1_t *_delegate;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtab;
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *iter;
+ int tid;
+ int pos;
+ int n_plp;
+ int mask;
+ const bam_pileup1_t * plp;
+ bam_plp_t pileup_iter;
+ __pyx_t_5pysam_9csamtools___iterdata iterdata;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ struct __pyx_obj_5pysam_9csamtools_Fastafile *fastafile;
+ PyObject *stepper;
+ int max_depth;
};
-/* "pysam/csamtools.pxd":438
- * cdef kseq_t * _delegate
+/* "pysam/csamtools.pxd":493
+ * cdef uint32_t _is_tail
+ *
+ * cdef class IteratorRow: # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class Fastqfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * cdef gzFile fastqfile
*/
-struct __pyx_obj_5pysam_9csamtools_Fastqfile {
+struct __pyx_obj_5pysam_9csamtools_IteratorRow {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtab;
- char *_filename;
- gzFile fastqfile;
- kseq_t *entry;
};
-/* "pysam/csamtools.pxd":523
- * cdef IteratorRowRegion rowiter
+/* "pysam/csamtools.pxd":496
+ * 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.pxd":570
+/* "pysam/csamtools.pxd":568
* pass
*
* cdef class IndexedReads: # <<<<<<<<<<<<<<
@@ -523,102 +527,113 @@ struct __pyx_obj_5pysam_9csamtools_IndexedReads {
};
-/* "pysam/csamtools.pxd":511
- * cdef int cnext(self)
+/* "pysam/csamtools.pyx":432
+ * data = [ x.split("\t") for x in inf ]
+ * self._references = tuple(x[0] for x in data)
+ * self._lengths = tuple(int(x[1]) for x in data) # <<<<<<<<<<<<<<
+ * self.reference2length = dict(zip(self._references, self._lengths))
*
- * 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;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr {
+ PyObject_HEAD
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *__pyx_outer_scope;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_t_0;
+ Py_ssize_t __pyx_t_1;
};
-/* "pysam/csamtools.pxd":535
- * cdef int cnext(self)
- *
- * cdef class IteratorColumn: # <<<<<<<<<<<<<<
+/* "pysam/csamtools.pyx":141
+ * 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])" )
*
- * # result of the last plbuf_push
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorColumn {
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtab;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *iter;
- int tid;
- int pos;
- int n_plp;
- int mask;
- const bam_pileup1_t * plp;
- bam_plp_t pileup_iter;
- __pyx_t_5pysam_9csamtools___iterdata iterdata;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- struct __pyx_obj_5pysam_9csamtools_Fastafile *fastafile;
- PyObject *stepper;
- int max_depth;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
-/* "pysam/csamtools.pxd":562
- * cdef reset( self, tid, start, end )
+/* "pysam/csamtools.pxd":436
+ * cdef kseq_t * _delegate
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * cdef int start
- * cdef int end
+ * cdef class Fastqfile: # <<<<<<<<<<<<<<
+ * cdef object _filename
+ * cdef gzFile fastqfile
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
- int start;
- int end;
- int truncate;
+struct __pyx_obj_5pysam_9csamtools_Fastqfile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtab;
+ PyObject *_filename;
+ gzFile fastqfile;
+ kseq_t *entry;
};
-/* "pysam/csamtools.pxd":451
- * cdef bam1_t * _delegate
+/* "pysam/csamtools.pxd":433
+ * cdef char* _fetch(self, char* reference, int start, int end, int* length)
+ *
+ * cdef class FastqProxy: # <<<<<<<<<<<<<<
+ * cdef kseq_t * _delegate
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
*/
-struct __pyx_obj_5pysam_9csamtools_Samfile {
+struct __pyx_obj_5pysam_9csamtools_FastqProxy {
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;
+ kseq_t *_delegate;
};
-/* "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.pyx":431
+ * with open( self._filename + b".fai" ) as inf:
+ * data = [ x.split("\t") for x in inf ]
+ * self._references = tuple(x[0] for x in data) # <<<<<<<<<<<<<<
+ * self._lengths = tuple(int(x[1]) for x in data)
+ * self.reference2length = dict(zip(self._references, self._lengths))
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr {
PyObject_HEAD
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *__pyx_outer_scope;
PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ Py_ssize_t __pyx_t_1;
+};
+
+
+/* "pysam/csamtools.pyx":411
+ * return faidx_fetch_nseq(self.fastafile)
+ *
+ * def _open(self, filename): # <<<<<<<<<<<<<<
+ * '''open an indexed fasta file.
+ *
+ */
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open {
+ PyObject_HEAD
+ PyObject *__pyx_v_data;
};
-/* "pysam/csamtools.pxd":567
+/* "pysam/csamtools.pxd":516
+ * 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;
+};
+
+
+/* "pysam/csamtools.pxd":565
* cdef int truncate
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
@@ -634,18 +649,89 @@ struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs {
* # Note: need to declare all C fields and methods here
* #
* cdef class Fastafile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to fastafile
+ * cdef object _filename, _references, _lengths, reference2length
+ * cdef faidx_t* fastafile
*/
struct __pyx_obj_5pysam_9csamtools_Fastafile {
PyObject_HEAD
struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtab;
- char *_filename;
+ PyObject *_filename;
+ PyObject *_references;
+ PyObject *_lengths;
+ PyObject *reference2length;
faidx_t *fastafile;
};
-/* "pysam/csamtools.pyx":140
+/* "pysam/csamtools.pxd":444
+ * cdef int cnext(self)
+ *
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ *
+ * # object that this AlignedRead represents
+ */
+struct __pyx_obj_5pysam_9csamtools_AlignedRead {
+ PyObject_HEAD
+ bam1_t *_delegate;
+};
+
+
+/* "pysam/csamtools.pxd":521
+ * 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_IteratorRowSelection *__pyx_vtab;
+ bam1_t *b;
+ int current_pos;
+ samfile_t *fp;
+ PyObject *positions;
+ int owns_samfile;
+};
+
+
+/* "pysam/csamtools.pxd":449
+ * cdef bam1_t * _delegate
+ *
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef object _filename
+ * # pointer to samfile
+ */
+struct __pyx_obj_5pysam_9csamtools_Samfile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtab;
+ PyObject *_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.pxd":560
+ * 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.pyx":139
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
@@ -662,7 +748,7 @@ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
};
-/* "pysam/csamtools.pxd":480
+/* "pysam/csamtools.pxd":478
* cdef char * _getrname( self, int tid )
*
* cdef class PileupProxy: # <<<<<<<<<<<<<<
@@ -678,59 +764,53 @@ struct __pyx_obj_5pysam_9csamtools_PileupProxy {
};
-/* "pysam/csamtools.pxd":486
- * cdef int n_pu
+/* "pysam/csamtools.pxd":509
+ * cdef int cnext(self)
*
- * cdef class PileupRead: # <<<<<<<<<<<<<<
- * cdef AlignedRead _alignment
- * cdef int32_t _qpos
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_PileupRead {
- 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;
+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":435
- * cdef char * _fetch( self, char * reference, int start, int end, int * length )
- *
- * cdef class FastqProxy: # <<<<<<<<<<<<<<
- * cdef kseq_t * _delegate
+
+/* "pysam/csamtools.pyx":381
+ * ## Public methods
+ * ######################################################################
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
*
*/
-struct __pyx_obj_5pysam_9csamtools_FastqProxy {
- PyObject_HEAD
- kseq_t *_delegate;
+
+struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
+ char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
};
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
-/* "pysam/csamtools.pxd":498
- * pass
+/* "pysam/csamtools.pyx":578
+ * else: return None
+ *
+ * cdef class Fastqfile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam_iter_t iter # iterator state object
- * cdef bam1_t * b
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
- bam1_t *b;
- int retval;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- samfile_t *fp;
- int owns_samfile;
-};
+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":1921
+/* "pysam/csamtools.pyx":1924
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
@@ -748,7 +828,7 @@ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn {
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
-/* "pysam/csamtools.pyx":2083
+/* "pysam/csamtools.pyx":2086
* self.iterdata.seq = NULL
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
@@ -762,22 +842,22 @@ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion {
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
-/* "pysam/csamtools.pyx":1597
- *
+/* "pysam/csamtools.pyx":1684
+ * if self.owns_samfile: samclose( self.fp )
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int reopen = True)*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
+struct __pyx_vtabstruct_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_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
-/* "pysam/csamtools.pyx":1792
+/* "pysam/csamtools.pyx":1795
* raise StopIteration
*
* cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
@@ -792,36 +872,25 @@ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection {
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
-/* "pysam/csamtools.pyx":382
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
- *
- */
-
-struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
- char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
-};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
-
-
-/* "pysam/csamtools.pyx":546
- * else: return None
+/* "pysam/csamtools.pyx":684
*
- * cdef class Fastqfile: # <<<<<<<<<<<<<<
- * '''*(filename)*
*
+ * 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_Fastqfile {
- kseq_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *);
+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_Fastqfile *__pyx_vtabptr_5pysam_9csamtools_Fastqfile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
-/* "pysam/csamtools.pyx":2120
+/* "pysam/csamtools.pyx":2123
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
@@ -835,37 +904,19 @@ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs {
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
-/* "pysam/csamtools.pyx":671
+/* "pysam/csamtools.pyx":1600
*
*
- * 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);
-};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
-
-
-/* "pysam/csamtools.pyx":1681
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
*
*/
-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_IteratorRowRegion {
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -992,19 +1043,7 @@ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*pr
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name); /*proto*/
-
-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact); /*proto*/
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname);
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
@@ -1108,6 +1147,25 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
#endif
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
+
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name); /*proto*/
+
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+ int result = PySequence_Contains(seq, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+}
+
+static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
+ const char *name, int exact); /*proto*/
+
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
if (unlikely(PyList_Append(L, x) < 0)) return NULL;
@@ -1131,11 +1189,6 @@ static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
- int result = PySequence_Contains(seq, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
-}
-
static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
int result = PyDict_Contains(dict, item);
return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
@@ -1505,12 +1558,15 @@ static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IndexedReads = 0;
static PyTypeObject *__pyx_ptype_5pysam_9csamtools_SNPCall = 0;
static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = 0;
static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_2__open = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_3_genexpr = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_4_genexpr = 0;
static PyObject *__pyx_v_5pysam_9csamtools__FILENAME_ENCODING = 0;
static char *__pyx_v_5pysam_9csamtools_CODE2CIGAR;
static char *__pyx_v_5pysam_9csamtools_bam_nt16_rev_table;
static int __pyx_v_5pysam_9csamtools_max_pos;
static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *, size_t); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools__encodeFilename(PyObject *); /*proto*/
static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *); /*proto*/
static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *); /*proto*/
@@ -1542,18 +1598,19 @@ static PyObject *__pyx_builtin_ord;
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IOError;
+static PyObject *__pyx_builtin_open;
+static PyObject *__pyx_builtin_zip;
+static PyObject *__pyx_builtin_IndexError;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_OverflowError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_OSError;
static PyObject *__pyx_builtin_AttributeError;
-static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_sorted;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_min;
static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_chr;
-static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_UnicodeDecodeError;
static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
@@ -1568,11 +1625,19 @@ static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON
static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_5_open_genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_5_open_3genexpr(PyObject *__pyx_self); /* proto */
static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_7lengths___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 PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_14getReferenceLength(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_16__getitem__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
+static int __pyx_pf_5pysam_9csamtools_9Fastafile_18__contains__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference); /* 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 */
@@ -1586,7 +1651,6 @@ static void __pyx_pf_5pysam_9csamtools_9Fastqfile_8__dealloc__(struct __pyx_obj_
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 */
@@ -1761,23 +1825,20 @@ static char __pyx_k_5[] = "\t";
static char __pyx_k_6[] = "\n";
static char __pyx_k_7[] = "calling len() on closed file";
static char __pyx_k_9[] = "could not open file `%s`";
-static char __pyx_k_10[] = "I/O operation on closed file";
-static char __pyx_k_13[] = "no sequence/region supplied.";
-static char __pyx_k_15[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_16[] = "";
-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_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_10[] = ".fai";
+static char __pyx_k_11[] = "could not locate index file";
+static char __pyx_k_15[] = "I/O operation on closed file";
+static char __pyx_k_17[] = "no sequence/region supplied.";
+static char __pyx_k_19[] = "invalid region: start (%i) > end (%i)";
+static char __pyx_k_20[] = "";
+static char __pyx_k_21[] = "start out of range (%i)";
+static char __pyx_k_22[] = "end out of range (%i)";
+static char __pyx_k_23[] = "%s:%i-%i";
+static char __pyx_k_25[] = "No such file or directory: %s";
+static char __pyx_k_30[] = "invalid file opening mode `%s`";
+static char __pyx_k_32[] = "-";
+static char __pyx_k_33[] = "http:";
+static char __pyx_k_35[] = "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";
@@ -1807,6 +1868,7 @@ 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_99[] = "Samfile.mapped only available in bam files";
static char __pyx_k__A[] = "A";
static char __pyx_k__B[] = "B";
static char __pyx_k__C[] = "C";
@@ -1827,108 +1889,108 @@ static char __pyx_k__n[] = "n";
static char __pyx_k__r[] = "r";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
-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 [...]
-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. [...]
-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 [...]
-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 algorit [...]
-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()` [...]
-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_101[] = "mapping information not recorded in index or index not available";
+static char __pyx_k_104[] = "Samfile.unmapped only available in bam files";
+static char __pyx_k_109[] = "@";
+static char __pyx_k_111[] = "header line without '@': '%s'";
+static char __pyx_k_113[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_114[] = ":";
+static char __pyx_k_115[] = "malformatted header: no ':' in field";
+static char __pyx_k_118[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_119[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_120[] = "@%s";
+static char __pyx_k_121[] = "%s:%s";
+static char __pyx_k_122[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_124[] = "incomplete sequence information in '%s'";
+static char __pyx_k_127[] = "can not iterate over samfile without header";
+static char __pyx_k_130[] = "no index available for iteration";
+static char __pyx_k_136[] = "can only use this iterator on bam files";
+static char __pyx_k_137[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_138[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_140[] = "error during iteration";
+static char __pyx_k_143[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_146[] = "%i%c";
+static char __pyx_k_147[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_148[] = "%c";
+static char __pyx_k_149[] = "<";
+static char __pyx_k_151[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_152[] = "2sccI%i%s";
+static char __pyx_k_156[] = "2sc%is";
+static char __pyx_k_158[] = "create_string_buffer";
+static char __pyx_k_159[] = "tag '%s' not present";
+static char __pyx_k_160[] = "unknown auxilliary type '%s'";
+static char __pyx_k_161[] = "Contig index";
+static char __pyx_k_162[] = "Mapped position on contig";
+static char __pyx_k_163[] = "Contig index for mate pair";
+static char __pyx_k_164[] = "Position of mate pair";
+static char __pyx_k_165[] = "Insert size";
+static char __pyx_k_166[] = "Binary flag";
+static char __pyx_k_167[] = "Count of cigar entries";
+static char __pyx_k_168[] = "Cigar entries";
+static char __pyx_k_169[] = "Mapping quality";
+static char __pyx_k_170[] = "Bam index bin number";
+static char __pyx_k_171[] = "Length of query name";
+static char __pyx_k_172[] = "Query name";
+static char __pyx_k_173[] = "Length of query sequence";
+static char __pyx_k_174[] = "Query sequence";
+static char __pyx_k_175[] = "Quality scores";
+static char __pyx_k_176[] = "Length of auxilary data";
+static char __pyx_k_177[] = "Maximum data length";
+static char __pyx_k_178[] = "Current data length";
+static char __pyx_k_179[] = "%-30s %-10s= %s";
+static char __pyx_k_180[] = "(";
+static char __pyx_k_181[] = ")";
+static char __pyx_k_182[] = "This class cannot be instantiated from Python";
+static char __pyx_k_184[] = "PileupProxy accessed after iterator finished";
+static char __pyx_k_188[] = "No such file or directory: '%s'";
+static char __pyx_k_189[] = "-o";
+static char __pyx_k_190[] = "option -o is forbidden in samtools view";
+static char __pyx_k_196[] = "can only IndexReads on bam files";
+static char __pyx_k_197[] = "read %s not found";
+static char __pyx_k_198[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_199[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_200[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_201[] = "tuple with the lengths of :term:`reference` sequences.";
+static char __pyx_k_202[] = "the query name (None if not present)";
+static char __pyx_k_203[] = "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 [...]
+static char __pyx_k_204[] = "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_205[] = "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. [...]
+static char __pyx_k_206[] = "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 [...]
+static char __pyx_k_207[] = "aligned portion of the read and excludes any flanking bases\n that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a\n unicode string to it consisting of ASCII characters only will\n 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 Smit [...]
+static char __pyx_k_208[] = "aligned query sequence quality values (None if not\n present). This property is read-only.\n\n In Python 3, this property is of type bytes.";
+static char __pyx_k_209[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_210[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_211[] = "Length of the aligned query sequence";
+static char __pyx_k_212[] = "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_213[] = "properties flag";
+static char __pyx_k_214[] = "\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()` [...]
+static char __pyx_k_215[] = "\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_216[] = "0-based leftmost coordinate";
+static char __pyx_k_217[] = "properties bin";
+static char __pyx_k_218[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_219[] = "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_220[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
+static char __pyx_k_221[] = "mapping quality";
+static char __pyx_k_222[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
+static char __pyx_k_223[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_224[] = "the position of the mate\n deprecated, use PNEXT instead.";
+static char __pyx_k_225[] = "the position of the mate";
+static char __pyx_k_226[] = "the insert size\n deprecated: use tlen instead";
+static char __pyx_k_227[] = "the insert size";
+static char __pyx_k_228[] = "true if read is paired in sequencing";
+static char __pyx_k_229[] = "true if read is mapped in a proper pair";
+static char __pyx_k_230[] = "true if read itself is unmapped";
+static char __pyx_k_231[] = "true if the mate is unmapped";
+static char __pyx_k_232[] = "true if read is mapped to reverse strand";
+static char __pyx_k_233[] = "true is read is mapped to reverse strand";
+static char __pyx_k_234[] = "true if this is read1";
+static char __pyx_k_235[] = "true if this is read2";
+static char __pyx_k_236[] = "true if not primary alignment";
+static char __pyx_k_237[] = "true if QC failure";
+static char __pyx_k_238[] = "true if optical or PCR duplicate";
+static char __pyx_k_239[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_240[] = "inferred read length from CIGAR string.\n\n Returns 0 if CIGAR string is not present.\n ";
+static char __pyx_k_241[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
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 ";
@@ -2066,6 +2128,7 @@ static char __pyx_k__bqual[] = "bqual";
static char __pyx_k__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
+static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__flush[] = "flush";
static char __pyx_k__indel[] = "indel";
static char __pyx_k__index[] = "index";
@@ -2179,6 +2242,7 @@ static char __pyx_k__traceback[] = "traceback";
static char __pyx_k__until_eof[] = "until_eof";
static char __pyx_k__CIGAR2CODE[] = "CIGAR2CODE";
static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3";
+static char __pyx_k__IndexError[] = "IndexError";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___buildLine[] = "_buildLine";
@@ -2224,39 +2288,37 @@ static char __pyx_k__getdefaultencoding[] = "getdefaultencoding";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
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_105;
-static PyObject *__pyx_kp_s_110;
-static PyObject *__pyx_kp_s_112;
+static PyObject *__pyx_kp_b_10;
+static PyObject *__pyx_kp_s_101;
+static PyObject *__pyx_kp_s_104;
+static PyObject *__pyx_kp_s_109;
+static PyObject *__pyx_kp_s_11;
+static PyObject *__pyx_kp_s_111;
+static PyObject *__pyx_kp_s_113;
static PyObject *__pyx_kp_s_114;
static PyObject *__pyx_kp_s_115;
-static PyObject *__pyx_kp_s_116;
+static PyObject *__pyx_kp_s_118;
static PyObject *__pyx_kp_s_119;
static PyObject *__pyx_kp_s_120;
static PyObject *__pyx_kp_s_121;
static PyObject *__pyx_kp_s_122;
-static PyObject *__pyx_kp_s_123;
-static PyObject *__pyx_kp_s_125;
-static PyObject *__pyx_kp_s_128;
-static PyObject *__pyx_kp_s_13;
-static PyObject *__pyx_kp_s_131;
+static PyObject *__pyx_kp_s_124;
+static PyObject *__pyx_kp_s_127;
+static PyObject *__pyx_kp_s_130;
+static PyObject *__pyx_kp_s_136;
static PyObject *__pyx_kp_s_137;
static PyObject *__pyx_kp_s_138;
-static PyObject *__pyx_kp_s_139;
-static PyObject *__pyx_kp_s_141;
+static PyObject *__pyx_kp_s_140;
+static PyObject *__pyx_kp_s_146;
static PyObject *__pyx_kp_s_147;
static PyObject *__pyx_kp_s_148;
static PyObject *__pyx_kp_s_149;
static PyObject *__pyx_kp_s_15;
-static PyObject *__pyx_kp_s_150;
+static PyObject *__pyx_kp_s_151;
static PyObject *__pyx_kp_s_152;
-static PyObject *__pyx_kp_s_153;
-static PyObject *__pyx_kp_s_157;
-static PyObject *__pyx_n_s_159;
-static PyObject *__pyx_kp_b_16;
-static PyObject *__pyx_kp_s_16;
+static PyObject *__pyx_kp_s_156;
+static PyObject *__pyx_n_s_158;
+static PyObject *__pyx_kp_s_159;
static PyObject *__pyx_kp_s_160;
static PyObject *__pyx_kp_s_161;
static PyObject *__pyx_kp_s_162;
@@ -2278,19 +2340,22 @@ static PyObject *__pyx_kp_s_176;
static PyObject *__pyx_kp_s_177;
static PyObject *__pyx_kp_s_178;
static PyObject *__pyx_kp_s_179;
-static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_180;
static PyObject *__pyx_kp_s_181;
static PyObject *__pyx_kp_s_182;
-static PyObject *__pyx_kp_s_183;
-static PyObject *__pyx_kp_s_185;
+static PyObject *__pyx_kp_s_184;
+static PyObject *__pyx_kp_s_188;
static PyObject *__pyx_kp_s_189;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_190;
-static PyObject *__pyx_kp_s_191;
+static PyObject *__pyx_kp_s_196;
static PyObject *__pyx_kp_s_197;
-static PyObject *__pyx_kp_s_198;
+static PyObject *__pyx_kp_b_20;
+static PyObject *__pyx_kp_s_20;
static PyObject *__pyx_kp_s_21;
+static PyObject *__pyx_kp_s_22;
+static PyObject *__pyx_kp_s_23;
+static PyObject *__pyx_kp_s_25;
static PyObject *__pyx_n_s_262;
static PyObject *__pyx_kp_s_264;
static PyObject *__pyx_kp_s_269;
@@ -2307,13 +2372,16 @@ static PyObject *__pyx_n_s_291;
static PyObject *__pyx_n_s_294;
static PyObject *__pyx_kp_s_295;
static PyObject *__pyx_kp_u_3;
+static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_n_s_304;
static PyObject *__pyx_n_s_307;
static PyObject *__pyx_n_s_310;
static PyObject *__pyx_n_s_313;
static PyObject *__pyx_n_s_316;
static PyObject *__pyx_kp_s_317;
-static PyObject *__pyx_kp_s_32;
+static PyObject *__pyx_kp_b_32;
+static PyObject *__pyx_kp_b_33;
+static PyObject *__pyx_kp_b_35;
static PyObject *__pyx_kp_s_37;
static PyObject *__pyx_kp_s_38;
static PyObject *__pyx_kp_s_39;
@@ -2347,6 +2415,7 @@ static PyObject *__pyx_kp_s_87;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_kp_s_90;
static PyObject *__pyx_kp_s_93;
+static PyObject *__pyx_kp_s_99;
static PyObject *__pyx_kp_s__2scB;
static PyObject *__pyx_kp_s__2scH;
static PyObject *__pyx_kp_s__2scI;
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static PyObject *__pyx_n_s__ID;
static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__IS_PYTHON3;
+static PyObject *__pyx_n_s__IndexError;
static PyObject *__pyx_n_s__IndexedReads;
static PyObject *__pyx_n_s__IteratorColumn;
static PyObject *__pyx_n_s__IteratorRow;
@@ -2482,6 +2552,7 @@ static PyObject *__pyx_n_s__extend;
static PyObject *__pyx_n_s__f;
static PyObject *__pyx_n_s__fastafile;
static PyObject *__pyx_n_s__fd;
+static PyObject *__pyx_n_s__fetch;
static PyObject *__pyx_n_s__fields;
static PyObject *__pyx_n_s__filename;
static PyObject *__pyx_n_s__fileno;
@@ -2642,23 +2713,26 @@ static PyObject *__pyx_int_neg_32767;
static PyObject *__pyx_int_536870912;
static PyObject *__pyx_int_4294967295;
static PyObject *__pyx_int_neg_2147483648;
+static PyObject *__pyx_k_27;
+static PyObject *__pyx_k_28;
static PyObject *__pyx_k_29;
-static PyObject *__pyx_k_30;
-static PyObject *__pyx_k_31;
static PyObject *__pyx_k_62;
static PyObject *__pyx_k_81;
-static int __pyx_k_140;
-static PyObject *__pyx_k_188;
+static int __pyx_k_139;
+static PyObject *__pyx_k_187;
static PyObject *__pyx_k_tuple_2;
static PyObject *__pyx_k_tuple_4;
static PyObject *__pyx_k_tuple_8;
-static PyObject *__pyx_k_tuple_11;
static PyObject *__pyx_k_tuple_12;
+static PyObject *__pyx_k_tuple_13;
static PyObject *__pyx_k_tuple_14;
-static PyObject *__pyx_k_tuple_20;
-static PyObject *__pyx_k_tuple_22;
-static PyObject *__pyx_k_tuple_23;
-static PyObject *__pyx_k_tuple_33;
+static PyObject *__pyx_k_tuple_16;
+static PyObject *__pyx_k_tuple_18;
+static PyObject *__pyx_k_tuple_24;
+static PyObject *__pyx_k_tuple_26;
+static PyObject *__pyx_k_tuple_31;
+static PyObject *__pyx_k_tuple_34;
+static PyObject *__pyx_k_tuple_36;
static PyObject *__pyx_k_tuple_47;
static PyObject *__pyx_k_tuple_48;
static PyObject *__pyx_k_tuple_50;
@@ -2690,45 +2764,44 @@ static PyObject *__pyx_k_tuple_95;
static PyObject *__pyx_k_tuple_96;
static PyObject *__pyx_k_tuple_97;
static PyObject *__pyx_k_tuple_98;
-static PyObject *__pyx_k_tuple_99;
-static PyObject *__pyx_k_tuple_101;
+static PyObject *__pyx_k_tuple_100;
+static PyObject *__pyx_k_tuple_102;
static PyObject *__pyx_k_tuple_103;
-static PyObject *__pyx_k_tuple_104;
+static PyObject *__pyx_k_tuple_105;
static PyObject *__pyx_k_tuple_106;
static PyObject *__pyx_k_tuple_107;
static PyObject *__pyx_k_tuple_108;
-static PyObject *__pyx_k_tuple_109;
-static PyObject *__pyx_k_tuple_111;
-static PyObject *__pyx_k_tuple_113;
+static PyObject *__pyx_k_tuple_110;
+static PyObject *__pyx_k_tuple_112;
+static PyObject *__pyx_k_tuple_116;
static PyObject *__pyx_k_tuple_117;
-static PyObject *__pyx_k_tuple_118;
-static PyObject *__pyx_k_tuple_124;
+static PyObject *__pyx_k_tuple_123;
+static PyObject *__pyx_k_tuple_125;
static PyObject *__pyx_k_tuple_126;
-static PyObject *__pyx_k_tuple_127;
+static PyObject *__pyx_k_tuple_128;
static PyObject *__pyx_k_tuple_129;
-static PyObject *__pyx_k_tuple_130;
+static PyObject *__pyx_k_tuple_131;
static PyObject *__pyx_k_tuple_132;
static PyObject *__pyx_k_tuple_133;
static PyObject *__pyx_k_tuple_134;
static PyObject *__pyx_k_tuple_135;
-static PyObject *__pyx_k_tuple_136;
+static PyObject *__pyx_k_tuple_141;
static PyObject *__pyx_k_tuple_142;
-static PyObject *__pyx_k_tuple_143;
+static PyObject *__pyx_k_tuple_144;
static PyObject *__pyx_k_tuple_145;
-static PyObject *__pyx_k_tuple_146;
-static PyObject *__pyx_k_tuple_151;
+static PyObject *__pyx_k_tuple_150;
+static PyObject *__pyx_k_tuple_153;
static PyObject *__pyx_k_tuple_154;
static PyObject *__pyx_k_tuple_155;
-static PyObject *__pyx_k_tuple_156;
-static PyObject *__pyx_k_tuple_158;
-static PyObject *__pyx_k_tuple_184;
+static PyObject *__pyx_k_tuple_157;
+static PyObject *__pyx_k_tuple_183;
+static PyObject *__pyx_k_tuple_185;
static PyObject *__pyx_k_tuple_186;
-static PyObject *__pyx_k_tuple_187;
+static PyObject *__pyx_k_tuple_191;
static PyObject *__pyx_k_tuple_192;
static PyObject *__pyx_k_tuple_193;
static PyObject *__pyx_k_tuple_194;
static PyObject *__pyx_k_tuple_195;
-static PyObject *__pyx_k_tuple_196;
static PyObject *__pyx_k_tuple_265;
static PyObject *__pyx_k_tuple_267;
static PyObject *__pyx_k_tuple_273;
@@ -2766,7 +2839,7 @@ static PyObject *__pyx_k_codeobj_315;
static PyObject *__pyx_k_codeobj_319;
static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-/* "pysam/csamtools.pyx":140
+/* "pysam/csamtools.pyx":139
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
@@ -2789,9 +2862,9 @@ static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__p
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
- __Pyx_TraceCall("genexpr", __pyx_f[0], 140);
+ __Pyx_TraceCall("genexpr", __pyx_f[0], 139);
{
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_cur_scope);
__Pyx_RefNannyFinishContext();
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@@ -2828,12 +2901,12 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
return NULL;
}
__pyx_L3_first_run:;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -2843,7 +2916,7 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
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if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -2859,12 +2932,12 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
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__Pyx_GIVEREF(__pyx_t_1);
__pyx_cur_scope->__pyx_v_x = __pyx_t_1;
- __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1);
__pyx_t_1 = __pyx_t_2;
__pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
@@ -2892,7 +2965,7 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
__pyx_cur_scope->__pyx_t_1 = 0;
__Pyx_XGOTREF(__pyx_t_3);
__pyx_t_4 = __pyx_cur_scope->__pyx_t_2;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -2912,7 +2985,7 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
}
static PyObject *__pyx_gb_5pysam_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-/* "pysam/csamtools.pyx":142
+/* "pysam/csamtools.pyx":141
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
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return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
- __Pyx_TraceCall("genexpr", __pyx_f[0], 142);
+ __Pyx_TraceCall("genexpr", __pyx_f[0], 141);
{
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_7generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_7generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_cur_scope);
__Pyx_RefNannyFinishContext();
return (PyObject *) gen;
@@ -2975,12 +3048,12 @@ static PyObject *__pyx_gb_5pysam_9csamtools_7generator1(__pyx_GeneratorObject *_
return NULL;
}
__pyx_L3_first_run:;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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__pyx_t_1 = (__pyx_v_filename == Py_None);
if (__pyx_t_1) {
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__pyx_t_1 = PyBytes_Check(__pyx_v_filename);
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__pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
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return __pyx_r;
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if (__pyx_t_1) {
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+ if (!(likely(PyBytes_CheckExact(__pyx_v_s))||((__pyx_v_s) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_s)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (__pyx_t_1) {
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+ if (!(likely(PyBytes_CheckExact(__pyx_v_s))||((__pyx_v_s) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_s)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":180
+ /* "pysam/csamtools.pyx":179
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos # <<<<<<<<<<<<<<
@@ -3908,7 +3981,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
__pyx_t_2 = __pyx_v_src->qpos;
__pyx_v_dest->_qpos = __pyx_t_2;
- /* "pysam/csamtools.pyx":181
+ /* "pysam/csamtools.pyx":180
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos
* dest._indel = src.indel # <<<<<<<<<<<<<<
@@ -3918,7 +3991,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
__pyx_t_3 = __pyx_v_src->indel;
__pyx_v_dest->_indel = __pyx_t_3;
- /* "pysam/csamtools.pyx":182
+ /* "pysam/csamtools.pyx":181
* dest._qpos = src.qpos
* dest._indel = src.indel
* dest._level = src.level # <<<<<<<<<<<<<<
@@ -3928,7 +4001,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
__pyx_t_3 = __pyx_v_src->level;
__pyx_v_dest->_level = __pyx_t_3;
- /* "pysam/csamtools.pyx":183
+ /* "pysam/csamtools.pyx":182
* dest._indel = src.indel
* dest._level = src.level
* dest._is_del = src.is_del # <<<<<<<<<<<<<<
@@ -3938,7 +4011,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
__pyx_t_4 = __pyx_v_src->is_del;
__pyx_v_dest->_is_del = __pyx_t_4;
- /* "pysam/csamtools.pyx":184
+ /* "pysam/csamtools.pyx":183
* dest._level = src.level
* dest._is_del = src.is_del
* dest._is_head = src.is_head # <<<<<<<<<<<<<<
@@ -3948,7 +4021,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
__pyx_t_4 = __pyx_v_src->is_head;
__pyx_v_dest->_is_head = __pyx_t_4;
- /* "pysam/csamtools.pyx":185
+ /* "pysam/csamtools.pyx":184
* dest._is_del = src.is_del
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail # <<<<<<<<<<<<<<
@@ -3958,7 +4031,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
__pyx_t_4 = __pyx_v_src->is_tail;
__pyx_v_dest->_is_tail = __pyx_t_4;
- /* "pysam/csamtools.pyx":186
+ /* "pysam/csamtools.pyx":185
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail
* return dest # <<<<<<<<<<<<<<
@@ -3984,7 +4057,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
return __pyx_r;
}
-/* "pysam/csamtools.pyx":189
+/* "pysam/csamtools.pyx":188
*
* cdef class FastqProxy
* cdef makeFastqProxy( kseq_t * src): # <<<<<<<<<<<<<<
@@ -4002,22 +4075,22 @@ static PyObject *__pyx_f_5pysam_9csamtools_makeFastqProxy(kseq_t *__pyx_v_src) {
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("makeFastqProxy", 0);
- __Pyx_TraceCall("makeFastqProxy", __pyx_f[0], 189);
+ __Pyx_TraceCall("makeFastqProxy", __pyx_f[0], 188);
- /* "pysam/csamtools.pyx":191
+ /* "pysam/csamtools.pyx":190
* cdef makeFastqProxy( kseq_t * src):
* '''enter src into AlignedRead.'''
* cdef FastqProxy dest = FastqProxy.__new__(FastqProxy) # <<<<<<<<<<<<<<
* dest._delegate = src
* return dest
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_FastqProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_FastqProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_FastqProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_FastqProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_FastqProxy *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":192
+ /* "pysam/csamtools.pyx":191
* '''enter src into AlignedRead.'''
* cdef FastqProxy dest = FastqProxy.__new__(FastqProxy)
* dest._delegate = src # <<<<<<<<<<<<<<
@@ -4026,7 +4099,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makeFastqProxy(kseq_t *__pyx_v_src) {
*/
__pyx_v_dest->_delegate = __pyx_v_src;
- /* "pysam/csamtools.pyx":193
+ /* "pysam/csamtools.pyx":192
* cdef FastqProxy dest = FastqProxy.__new__(FastqProxy)
* dest._delegate = src
* return dest # <<<<<<<<<<<<<<
@@ -4052,7 +4125,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makeFastqProxy(kseq_t *__pyx_v_src) {
return __pyx_r;
}
-/* "pysam/csamtools.pyx":195
+/* "pysam/csamtools.pyx":194
* return dest
*
* cdef convertBinaryTagToList( uint8_t * s ): # <<<<<<<<<<<<<<
@@ -4079,9 +4152,9 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("convertBinaryTagToList", 0);
- __Pyx_TraceCall("convertBinaryTagToList", __pyx_f[0], 195);
+ __Pyx_TraceCall("convertBinaryTagToList", __pyx_f[0], 194);
- /* "pysam/csamtools.pyx":202
+ /* "pysam/csamtools.pyx":201
*
* # get byte size
* auxtype = s[0] # <<<<<<<<<<<<<<
@@ -4090,7 +4163,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
*/
__pyx_v_auxtype = (__pyx_v_s[0]);
- /* "pysam/csamtools.pyx":203
+ /* "pysam/csamtools.pyx":202
* # get byte size
* auxtype = s[0]
* byte_size = bam_aux_type2size( auxtype ) # <<<<<<<<<<<<<<
@@ -4099,7 +4172,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
*/
__pyx_v_byte_size = bam_aux_type2size(__pyx_v_auxtype);
- /* "pysam/csamtools.pyx":204
+ /* "pysam/csamtools.pyx":203
* auxtype = s[0]
* byte_size = bam_aux_type2size( auxtype )
* s += 1 # <<<<<<<<<<<<<<
@@ -4108,7 +4181,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "pysam/csamtools.pyx":206
+ /* "pysam/csamtools.pyx":205
* s += 1
* # get number of values in array
* nvalues = (<int32_t*>s)[0] # <<<<<<<<<<<<<<
@@ -4117,7 +4190,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
*/
__pyx_v_nvalues = (((int32_t *)__pyx_v_s)[0]);
- /* "pysam/csamtools.pyx":207
+ /* "pysam/csamtools.pyx":206
* # get number of values in array
* nvalues = (<int32_t*>s)[0]
* s += 4 # <<<<<<<<<<<<<<
@@ -4126,19 +4199,19 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
*/
__pyx_v_s = (__pyx_v_s + 4);
- /* "pysam/csamtools.pyx":209
+ /* "pysam/csamtools.pyx":208
* s += 4
* # get values
* values = [] # <<<<<<<<<<<<<<
* if auxtype == 'c':
* for x from 0 <= x < nvalues:
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_values = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":210
+ /* "pysam/csamtools.pyx":209
* # get values
* values = []
* if auxtype == 'c': # <<<<<<<<<<<<<<
@@ -4148,7 +4221,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_2 = (__pyx_v_auxtype == 'c');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":211
+ /* "pysam/csamtools.pyx":210
* values = []
* if auxtype == 'c':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -4158,19 +4231,19 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":212
+ /* "pysam/csamtools.pyx":211
* if auxtype == 'c':
* for x from 0 <= x < nvalues:
* values.append((<int8_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype == 'C':
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_int8_t((((int8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int8_t((((int8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":213
+ /* "pysam/csamtools.pyx":212
* for x from 0 <= x < nvalues:
* values.append((<int8_t*>s)[0])
* s += 1 # <<<<<<<<<<<<<<
@@ -4182,7 +4255,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":214
+ /* "pysam/csamtools.pyx":213
* values.append((<int8_t*>s)[0])
* s += 1
* elif auxtype == 'C': # <<<<<<<<<<<<<<
@@ -4192,7 +4265,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_2 = (__pyx_v_auxtype == 'C');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":215
+ /* "pysam/csamtools.pyx":214
* s += 1
* elif auxtype == 'C':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -4202,19 +4275,19 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":216
+ /* "pysam/csamtools.pyx":215
* elif auxtype == 'C':
* for x from 0 <= x < nvalues:
* values.append((<uint8_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype == 's':
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((((uint8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((((uint8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":217
+ /* "pysam/csamtools.pyx":216
* for x from 0 <= x < nvalues:
* values.append((<uint8_t*>s)[0])
* s += 1 # <<<<<<<<<<<<<<
@@ -4226,7 +4299,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":218
+ /* "pysam/csamtools.pyx":217
* values.append((<uint8_t*>s)[0])
* s += 1
* elif auxtype == 's': # <<<<<<<<<<<<<<
@@ -4236,7 +4309,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_2 = (__pyx_v_auxtype == 's');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":219
+ /* "pysam/csamtools.pyx":218
* s += 1
* elif auxtype == 's':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -4246,19 +4319,19 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":220
+ /* "pysam/csamtools.pyx":219
* elif auxtype == 's':
* for x from 0 <= x < nvalues:
* values.append((<int16_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype == 'S':
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":221
+ /* "pysam/csamtools.pyx":220
* for x from 0 <= x < nvalues:
* values.append((<int16_t*>s)[0])
* s += 2 # <<<<<<<<<<<<<<
@@ -4270,7 +4343,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":222
+ /* "pysam/csamtools.pyx":221
* values.append((<int16_t*>s)[0])
* s += 2
* elif auxtype == 'S': # <<<<<<<<<<<<<<
@@ -4280,7 +4353,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_2 = (__pyx_v_auxtype == 'S');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":223
+ /* "pysam/csamtools.pyx":222
* s += 2
* elif auxtype == 'S':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -4290,19 +4363,19 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":224
+ /* "pysam/csamtools.pyx":223
* elif auxtype == 'S':
* for x from 0 <= x < nvalues:
* values.append((<uint16_t*>s)[0]) # <<<<<<<<<<<<<<
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* elif auxtype == 'i':
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":225
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* for x from 0 <= x < nvalues:
* values.append((<uint16_t*>s)[0])
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@@ -4314,7 +4387,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
goto __pyx_L3;
}
- /* "pysam/csamtools.pyx":226
+ /* "pysam/csamtools.pyx":225
* values.append((<uint16_t*>s)[0])
* s += 2
* elif auxtype == 'i': # <<<<<<<<<<<<<<
@@ -4324,7 +4397,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_2 = (__pyx_v_auxtype == 'i');
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":227
+ /* "pysam/csamtools.pyx":226
* s += 2
* elif auxtype == 'i':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -4334,19 +4407,19 @@ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":228
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* elif auxtype == 'i':
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__Pyx_RefNannySetupContext("_hasIndex", 0);
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+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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values[1] = ((PyObject *)Py_None);
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values[2] = (PyObject *)((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None);
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Py_ssize_t kw_args;
const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
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__Pyx_INCREF(__pyx_v_referencenames);
__Pyx_INCREF(__pyx_v_text);
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- if (__pyx_t_11) {
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- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_10 = __pyx_t_11;
+ __pyx_t_11 = __pyx_t_1;
}
- if (unlikely(!__pyx_t_10)) {
+ if (unlikely(!__pyx_t_11)) {
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_37));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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- /* "pysam/csamtools.pyx":817
+ /* "pysam/csamtools.pyx":822
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* assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"
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* # allocate and fill header
*/
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- __pyx_t_13 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_15 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!(__pyx_t_13 == __pyx_t_15))) {
+ __pyx_t_12 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!(__pyx_t_12 == __pyx_t_14))) {
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_38));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":820
+ /* "pysam/csamtools.pyx":825
*
* # allocate and fill header
* referencenames = [ _force_bytes(ref) for ref in referencenames ] # <<<<<<<<<<<<<<
* header_to_write = bam_header_init()
* header_to_write.n_targets = len(referencenames)
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- __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
- __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
- __pyx_t_16 = NULL;
+ __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0;
+ __pyx_t_15 = NULL;
} else {
- __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_16 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_8)) break;
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- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
} else {
- __pyx_t_7 = __pyx_t_16(__pyx_t_8);
+ __pyx_t_7 = __pyx_t_15(__pyx_t_8);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
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__pyx_t_7 = 0;
- __pyx_t_7 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
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+ if (unlikely(__Pyx_PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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__pyx_v_referencenames = __pyx_t_8;
__pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":821
+ /* "pysam/csamtools.pyx":826
* # allocate and fill header
* referencenames = [ _force_bytes(ref) for ref in referencenames ]
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*/
__pyx_v_header_to_write = bam_header_init();
- /* "pysam/csamtools.pyx":822
+ /* "pysam/csamtools.pyx":827
* referencenames = [ _force_bytes(ref) for ref in referencenames ]
* header_to_write = bam_header_init()
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- __pyx_v_header_to_write->n_targets = __pyx_t_15;
+ __pyx_t_14 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->n_targets = __pyx_t_14;
- /* "pysam/csamtools.pyx":823
+ /* "pysam/csamtools.pyx":828
* header_to_write = bam_header_init()
* header_to_write.n_targets = len(referencenames)
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__Pyx_INCREF(__pyx_int_0);
__pyx_v_n = __pyx_int_0;
- /* "pysam/csamtools.pyx":824
+ /* "pysam/csamtools.pyx":829
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- __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
- __pyx_t_16 = NULL;
+ __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0;
+ __pyx_t_15 = NULL;
} else {
- __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_16 = Py_TYPE(__pyx_t_8)->tp_iternext;
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for (;;) {
- if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
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- __pyx_t_5 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_8, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
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#endif
} else {
- __pyx_t_5 = __pyx_t_16(__pyx_t_8);
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if (unlikely(!__pyx_t_5)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
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break;
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+ __pyx_t_12 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_v_n);
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}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "pysam/csamtools.pyx":825
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* for x in referencenames: n += len(x) + 1
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- __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_17, (sizeof(char *))));
+ __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_16, (sizeof(char *))));
- /* "pysam/csamtools.pyx":826
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PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_int_1);
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__Pyx_RefNannySetupContext("reset", 0);
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+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
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__Pyx_GIVEREF(__pyx_int_0);
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if (__pyx_t_4) {
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__pyx_L4:;
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PyObject* values[6] = {0,0,0,0,0,0};
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values[0] = ((PyObject *)Py_None);
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values[1] = ((PyObject *)Py_None);
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values[2] = ((PyObject *)Py_None);
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*/
values[3] = ((PyObject *)Py_None);
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}
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}
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PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
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*/
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*/
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*/
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@@ -12718,7 +13511,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
Py_ssize_t i;
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+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
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{
Py_ssize_t index = -1;
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+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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@@ -12737,7 +13530,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
__Pyx_GOTREF(item);
*(temps[index]) = item;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_v_region);
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@@ -12761,7 +13554,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
__pyx_v_rstart = __pyx_t_11;
__pyx_v_rend = __pyx_t_12;
- /* "pysam/csamtools.pyx":1167
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@@ -12770,7 +13563,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
*/
__pyx_v_counter = 0;
- /* "pysam/csamtools.pyx":1169
+ /* "pysam/csamtools.pyx":1174
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@@ -12779,22 +13572,22 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
*/
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- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
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+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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if (__pyx_t_13) {
@@ -12809,75 +13602,75 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
}
if (__pyx_t_13) {
- /* "pysam/csamtools.pyx":1171
+ /* "pysam/csamtools.pyx":1176
* if self.isbam:
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* if not region:
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- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_83), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_83), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L7;
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__pyx_L7:;
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+ /* "pysam/csamtools.pyx":1178
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- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_13);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1174
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*
* if not region:
* raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
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- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_85), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_85), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
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__pyx_L8:;
- /* "pysam/csamtools.pyx":1175
+ /* "pysam/csamtools.pyx":1180
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- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
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+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L9;
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__pyx_L9:;
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- /* "pysam/csamtools.pyx":1183
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- __pyx_t_5 = PyInt_FromLong(__pyx_v_counter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_counter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
@@ -12903,18 +13696,18 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
}
/*else*/ {
- /* "pysam/csamtools.pyx":1185
+ /* "pysam/csamtools.pyx":1190
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* def pileup( self,
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- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_88), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_88), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_L6:;
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PyObject* values[5] = {0,0,0,0,0};
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*/
values[0] = ((PyObject *)Py_None);
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*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1190
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*/
values[2] = ((PyObject *)Py_None);
- /* "pysam/csamtools.pyx":1191
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*/
values[3] = ((PyObject *)Py_None);
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}
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+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -13062,7 +13855,7 @@ static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
__Pyx_AddTraceback("pysam.csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
@@ -13075,7 +13868,7 @@ static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1187
+/* "pysam/csamtools.pyx":1192
* raise ValueError ("count for a region is not available for sam files" )
*
* def pileup( self, # <<<<<<<<<<<<<<
@@ -13109,51 +13902,51 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("pileup", 0);
- __Pyx_TraceCall("pileup", __pyx_f[0], 1187);
+ __Pyx_TraceCall("pileup", __pyx_f[0], 1192);
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* cdef bam_plbuf_t *buf
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* if not self._isOpen(): # <<<<<<<<<<<<<<
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+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
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+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":1244
+ /* "pysam/csamtools.pyx":1249
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
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* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
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- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L3;
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__pyx_L3:;
- /* "pysam/csamtools.pyx":1246
+ /* "pysam/csamtools.pyx":1251
* raise ValueError( "I/O operation on closed file" )
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
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* if self.isbam:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
@@ -13167,7 +13960,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -13181,7 +13974,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
if (unlikely(size != 4)) {
if (size > 4) __Pyx_RaiseTooManyValuesError(4);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -13203,7 +13996,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
Py_ssize_t i;
PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
for (i=0; i < 4; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
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@@ -13213,7 +14006,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
{
Py_ssize_t index = -1;
PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
- __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
@@ -13222,7 +14015,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
__Pyx_GOTREF(item);
*(temps[index]) = item;
}
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L5_unpacking_done;
@@ -13230,23 +14023,23 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_9 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
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+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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__pyx_v_rtid = __pyx_t_11;
__pyx_v_rstart = __pyx_t_12;
__pyx_v_rend = __pyx_t_13;
- /* "pysam/csamtools.pyx":1248
+ /* "pysam/csamtools.pyx":1253
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*
* if self.isbam: # <<<<<<<<<<<<<<
@@ -13255,42 +14048,42 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
*/
if (__pyx_v_self->isbam) {
- /* "pysam/csamtools.pyx":1249
+ /* "pysam/csamtools.pyx":1254
*
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*
* if callback:
*/
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+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_91), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L7;
}
__pyx_L7:;
- /* "pysam/csamtools.pyx":1251
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* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
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+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1252
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*
* if callback:
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@@ -13299,16 +14092,16 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
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__pyx_t_3 = (!__pyx_v_has_coord);
if (__pyx_t_3) {
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_92), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_92), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L9;
}
__pyx_L9:;
- /* "pysam/csamtools.pyx":1254
+ /* "pysam/csamtools.pyx":1259
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
*
* buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback ) # <<<<<<<<<<<<<<
@@ -13317,7 +14110,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
*/
__pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_5pysam_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
- /* "pysam/csamtools.pyx":1257
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*/
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- /* "pysam/csamtools.pyx":1260
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*
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@@ -13335,7 +14128,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
*/
bam_plbuf_push(NULL, __pyx_v_buf);
- /* "pysam/csamtools.pyx":1261
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@@ -13347,7 +14140,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
}
/*else*/ {
- /* "pysam/csamtools.pyx":1263
+ /* "pysam/csamtools.pyx":1268
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#else
- __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
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+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (PyErr_Occurred()) {
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__Pyx_Raise(__pyx_t_9, 0, 0, 0);
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+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_key = __pyx_t_2;
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+ __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_v_fields, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
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+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
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+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
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+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
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__Pyx_GIVEREF(__pyx_t_2);
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+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_121), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
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+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
goto __pyx_L8;
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@@ -16060,7 +16798,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1461
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+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_fields); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
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if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
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+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
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+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_2 = __pyx_t_6(__pyx_t_1);
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+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_8 = (!__pyx_t_3);
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- /* "pysam/csamtools.pyx":1463
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PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
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+ __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else {
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break;
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__pyx_v_fields = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1493
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+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
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+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
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__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
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+ __pyx_t_11 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
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__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__Pyx_GOTREF(__pyx_t_2);
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__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
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+ __pyx_t_6 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
if (PyList_CheckExact(__pyx_t_6) || PyTuple_CheckExact(__pyx_t_6)) {
__pyx_t_2 = __pyx_t_6; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
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+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
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+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
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+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else {
__pyx_t_6 = __pyx_t_4(__pyx_t_2);
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if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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break;
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@@ -16596,7 +17334,7 @@ static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __py
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if (size > 2) __Pyx_RaiseTooManyValuesError(2);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (likely(PyTuple_CheckExact(sequence))) {
@@ -16609,16 +17347,16 @@ static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __py
__Pyx_INCREF(__pyx_t_11);
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+ __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
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+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
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+ __pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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@@ -16626,7 +17364,7 @@ static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __py
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+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L13_unpacking_done;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_t_6, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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strncpy(__pyx_v_dest->text, __pyx_t_13, __pyx_v_dest->l_text);
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+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else {
__pyx_t_7 = __pyx_t_4(__pyx_t_1);
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- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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break;
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__pyx_v_fields = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/csamtools.pyx":1516
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- /* "pysam/csamtools.pyx":1517
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__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
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__Pyx_GIVEREF(__pyx_t_2);
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__pyx_t_2 = 0;
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+ __pyx_t_8 = PyList_Append(__pyx_v_seqs, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1520; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
}
__Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
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__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/csamtools.pyx":1518
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/csamtools.pyx":1519
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__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
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PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11));
__Pyx_GIVEREF(((PyObject *)__pyx_t_11));
__pyx_t_11 = 0;
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+ __pyx_t_11 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1522; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_GOTREF(__pyx_t_11);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1519; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
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}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs)); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest->n_targets = __pyx_t_3;
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*/
__pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *))));
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* dest.n_targets = len(seqs)
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__pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t))));
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for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_19; __pyx_v_x++) {
- /* "pysam/csamtools.pyx":1526
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+ __pyx_t_1 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
PyObject* sequence = __pyx_t_1;
@@ -17099,7 +17837,7 @@ static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __py
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if (size > 2) __Pyx_RaiseTooManyValuesError(2);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -17112,16 +17850,16 @@ static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __py
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+ __pyx_t_7 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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int __pyx_t_3;
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((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
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+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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bam_destroy1(__pyx_v_self->b);
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bam_iter_destroy(__pyx_v_self->iter);
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int __pyx_t_3;
int __pyx_t_4;
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((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self->rowiter->__pyx_vtab)->cnext(__pyx_v_self->rowiter);
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+/* "pysam/csamtools.pyx":1868
* ##-------------------------------------------------------------------
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* cdef int __advance_all( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
@@ -19810,9 +20554,9 @@ static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *_
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__advance_all", 0);
- __Pyx_TraceCall("__advance_all", __pyx_f[0], 1865);
+ __Pyx_TraceCall("__advance_all", __pyx_f[0], 1868);
- /* "pysam/csamtools.pyx":1869
+ /* "pysam/csamtools.pyx":1872
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
@@ -19821,7 +20565,7 @@ static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *_
*/
__pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
- /* "pysam/csamtools.pyx":1870
+ /* "pysam/csamtools.pyx":1873
* cdef __iterdata * d
* d = <__iterdata*>data
* return bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -19838,7 +20582,7 @@ static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *_
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1872
+/* "pysam/csamtools.pyx":1875
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
@@ -19869,9 +20613,9 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__advance_snpcalls", 0);
- __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1872);
+ __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1875);
- /* "pysam/csamtools.pyx":1877
+ /* "pysam/csamtools.pyx":1880
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
@@ -19880,7 +20624,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
- /* "pysam/csamtools.pyx":1879
+ /* "pysam/csamtools.pyx":1882
* d = <__iterdata*>data
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -19889,7 +20633,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
- /* "pysam/csamtools.pyx":1880
+ /* "pysam/csamtools.pyx":1883
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
* cdef int skip = 0 # <<<<<<<<<<<<<<
@@ -19898,7 +20642,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1882
+ /* "pysam/csamtools.pyx":1885
* cdef int skip = 0
* cdef int q
* cdef int is_cns = 1 # <<<<<<<<<<<<<<
@@ -19907,7 +20651,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_is_cns = 1;
- /* "pysam/csamtools.pyx":1883
+ /* "pysam/csamtools.pyx":1886
* cdef int q
* cdef int is_cns = 1
* cdef int is_nobaq = 0 # <<<<<<<<<<<<<<
@@ -19916,7 +20660,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_is_nobaq = 0;
- /* "pysam/csamtools.pyx":1884
+ /* "pysam/csamtools.pyx":1887
* cdef int is_cns = 1
* cdef int is_nobaq = 0
* cdef int capQ_thres = 0 # <<<<<<<<<<<<<<
@@ -19925,7 +20669,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_capQ_thres = 0;
- /* "pysam/csamtools.pyx":1887
+ /* "pysam/csamtools.pyx":1890
*
* # reload sequence
* if d.fastafile != NULL and b.core.tid != d.tid: # <<<<<<<<<<<<<<
@@ -19941,7 +20685,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1888
+ /* "pysam/csamtools.pyx":1891
* # reload sequence
* if d.fastafile != NULL and b.core.tid != d.tid:
* if d.seq != NULL: free(d.seq) # <<<<<<<<<<<<<<
@@ -19955,7 +20699,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L4:;
- /* "pysam/csamtools.pyx":1889
+ /* "pysam/csamtools.pyx":1892
* if d.fastafile != NULL and b.core.tid != d.tid:
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid # <<<<<<<<<<<<<<
@@ -19965,7 +20709,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__pyx_t_4 = __pyx_v_b->core.tid;
__pyx_v_d->tid = __pyx_t_4;
- /* "pysam/csamtools.pyx":1890
+ /* "pysam/csamtools.pyx":1893
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid
* d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<<
@@ -19974,7 +20718,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_5pysam_9csamtools_max_pos, (&__pyx_v_d->seq_len));
- /* "pysam/csamtools.pyx":1894
+ /* "pysam/csamtools.pyx":1897
* 0, max_pos,
* &d.seq_len)
* if d.seq == NULL: # <<<<<<<<<<<<<<
@@ -19984,26 +20728,26 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__pyx_t_3 = (__pyx_v_d->seq == NULL);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1896
+ /* "pysam/csamtools.pyx":1899
* if d.seq == NULL:
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
* (d.samfile.header.target_name[d.tid], # <<<<<<<<<<<<<<
* d.tid))
*
*/
- __pyx_t_5 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- /* "pysam/csamtools.pyx":1897
+ /* "pysam/csamtools.pyx":1900
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
* (d.samfile.header.target_name[d.tid],
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*
*
*/
- __pyx_t_6 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
@@ -20011,20 +20755,20 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_138), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
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__pyx_L5:;
@@ -20032,7 +20776,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1900
+ /* "pysam/csamtools.pyx":1903
*
*
* while ret >= 0: # <<<<<<<<<<<<<<
@@ -20043,7 +20787,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__pyx_t_3 = (__pyx_v_ret >= 0);
if (!__pyx_t_3) break;
- /* "pysam/csamtools.pyx":1902
+ /* "pysam/csamtools.pyx":1905
* while ret >= 0:
*
* skip = 0 # <<<<<<<<<<<<<<
@@ -20052,7 +20796,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1905
+ /* "pysam/csamtools.pyx":1908
*
* # realign read - changes base qualities
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq ) # <<<<<<<<<<<<<<
@@ -20077,7 +20821,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L8:;
- /* "pysam/csamtools.pyx":1907
+ /* "pysam/csamtools.pyx":1910
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq )
*
* if d.seq != NULL and capQ_thres > 10: # <<<<<<<<<<<<<<
@@ -20093,7 +20837,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":1908
+ /* "pysam/csamtools.pyx":1911
*
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
@@ -20102,7 +20846,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
- /* "pysam/csamtools.pyx":1909
+ /* "pysam/csamtools.pyx":1912
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1 # <<<<<<<<<<<<<<
@@ -20115,7 +20859,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
goto __pyx_L10;
}
- /* "pysam/csamtools.pyx":1910
+ /* "pysam/csamtools.pyx":1913
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q # <<<<<<<<<<<<<<
@@ -20132,7 +20876,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L9:;
- /* "pysam/csamtools.pyx":1911
+ /* "pysam/csamtools.pyx":1914
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1 # <<<<<<<<<<<<<<
@@ -20145,7 +20889,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
goto __pyx_L11;
}
- /* "pysam/csamtools.pyx":1912
+ /* "pysam/csamtools.pyx":1915
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 # <<<<<<<<<<<<<<
@@ -20164,7 +20908,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L11:;
- /* "pysam/csamtools.pyx":1914
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* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
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* if not skip: break # <<<<<<<<<<<<<<
@@ -20178,7 +20922,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L12:;
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* # additional filters
*
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}
__pyx_L7_break:;
- /* "pysam/csamtools.pyx":1919
+ /* "pysam/csamtools.pyx":1922
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* return ret # <<<<<<<<<<<<<<
@@ -20241,7 +20985,7 @@ static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__py
else goto __pyx_L5_argtuple_error;
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if (unlikely(kw_args > 0)) {
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+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1971; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -20252,14 +20996,14 @@ static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__py
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goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1971; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
__Pyx_AddTraceback("pysam.csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
goto __pyx_L0;
__pyx_L1_error:;
@@ -20270,7 +21014,7 @@ static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__py
return __pyx_r;
}
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+/* "pysam/csamtools.pyx":1971
* '''
*
* def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
@@ -20289,9 +21033,9 @@ static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_ob
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1968);
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- /* "pysam/csamtools.pyx":1969
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*
* def __cinit__( self, Samfile samfile, **kwargs ):
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__Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
__pyx_v_self->samfile = __pyx_v_samfile;
- /* "pysam/csamtools.pyx":1970
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* def __cinit__( self, Samfile samfile, **kwargs ):
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}
/*else*/ {
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+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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}
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}
__pyx_L4:;
- /* "pysam/csamtools.pyx":2064
+ /* "pysam/csamtools.pyx":2067
* if self.tid != tid:
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* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
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*/
__pyx_v_self->iterdata.seq = NULL;
- /* "pysam/csamtools.pyx":2065
+ /* "pysam/csamtools.pyx":2068
* if self.iterdata.seq != NULL: free( self.iterdata.seq )
* self.iterdata.seq = NULL
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
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}
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__Pyx_RefNannyFinishContext();
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* def __dealloc__(self): # <<<<<<<<<<<<<<
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int __pyx_t_1;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 2070);
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@@ -21222,7 +21966,7 @@ static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __py
__pyx_t_1 = (__pyx_v_self->pileup_iter != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2074
+ /* "pysam/csamtools.pyx":2077
* # that have not been fully consumed
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* bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
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*/
bam_plp_reset(__pyx_v_self->pileup_iter);
- /* "pysam/csamtools.pyx":2075
+ /* "pysam/csamtools.pyx":2078
* if self.pileup_iter != <bam_plp_t>NULL:
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter) # <<<<<<<<<<<<<<
@@ -21240,7 +21984,7 @@ static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __py
*/
bam_plp_destroy(__pyx_v_self->pileup_iter);
- /* "pysam/csamtools.pyx":2076
+ /* "pysam/csamtools.pyx":2079
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter)
* self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
@@ -21249,7 +21993,7 @@ static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __py
*/
__pyx_v_self->pileup_iter = NULL;
- /* "pysam/csamtools.pyx":2077
+ /* "pysam/csamtools.pyx":2080
* bam_plp_destroy(self.pileup_iter)
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* self.plp = <const_bam_pileup1_t_ptr>NULL # <<<<<<<<<<<<<<
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}
__pyx_L3:;
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* self.plp = <const_bam_pileup1_t_ptr>NULL
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* if self.iterdata.seq != NULL: # <<<<<<<<<<<<<<
@@ -21271,7 +22015,7 @@ static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __py
__pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2080
+ /* "pysam/csamtools.pyx":2083
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* if self.iterdata.seq != NULL:
* free(self.iterdata.seq) # <<<<<<<<<<<<<<
@@ -21280,7 +22024,7 @@ static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __py
*/
free(__pyx_v_self->iterdata.seq);
- /* "pysam/csamtools.pyx":2081
+ /* "pysam/csamtools.pyx":2084
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* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
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}
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+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2089; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -21367,25 +22111,25 @@ static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject
}
__pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
if (values[1]) {
- __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2087; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2090; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_tid = ((int)0);
}
if (values[2]) {
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+ __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2091; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_start = ((int)0);
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if (values[3]) {
- __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2089; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
- __pyx_v_end = __pyx_k_140;
+ __pyx_v_end = __pyx_k_139;
}
if (values[4]) {
- __pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2090; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2093; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
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* int start = 0,
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}
goto __pyx_L4_argument_unpacking_done;
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- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2089; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
__Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_truncate, __pyx_v_kwargs);
goto __pyx_L0;
__pyx_L1_error:;
@@ -21415,7 +22159,7 @@ static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject
return __pyx_r;
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-/* "pysam/csamtools.pyx":2086
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* '''iterates over a region only.
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* def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
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int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 2086);
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*/
__pyx_t_2.__pyx_n = 1;
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+ __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2097; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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*/
__pyx_v_self->start = __pyx_v_start;
- /* "pysam/csamtools.pyx":2096
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*/
__pyx_v_self->end = __pyx_v_end;
- /* "pysam/csamtools.pyx":2097
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return __pyx_r;
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while (1) {
if (!1) break;
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((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
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__pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2106
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goto __pyx_L5;
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2127; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
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+ __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_5pysam_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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while (1) {
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((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
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__pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
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__pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL);
if (__pyx_t_1) {
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__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
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*/
case 5:
- /* "pysam/csamtools.pyx":2171
+ /* "pysam/csamtools.pyx":2174
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -22083,16 +22827,16 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2172
+ /* "pysam/csamtools.pyx":2175
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
* return -1
* elif op==BAM_CSOFT_CLIP:
*/
- PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_144);
+ PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_143);
- /* "pysam/csamtools.pyx":2173
+ /* "pysam/csamtools.pyx":2176
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
@@ -22106,7 +22850,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2174
+ /* "pysam/csamtools.pyx":2177
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -22115,7 +22859,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
*/
case 4:
- /* "pysam/csamtools.pyx":2175
+ /* "pysam/csamtools.pyx":2178
* return -1
* elif op==BAM_CSOFT_CLIP:
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
@@ -22126,7 +22870,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
break;
default:
- /* "pysam/csamtools.pyx":2177
+ /* "pysam/csamtools.pyx":2180
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
@@ -22142,7 +22886,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2179
+ /* "pysam/csamtools.pyx":2182
* break
*
* return start_offset # <<<<<<<<<<<<<<
@@ -22159,7 +22903,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2184
+/* "pysam/csamtools.pyx":2187
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
@@ -22180,9 +22924,9 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
int __pyx_t_4;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("query_end", 0);
- __Pyx_TraceCall("query_end", __pyx_f[0], 2184);
+ __Pyx_TraceCall("query_end", __pyx_f[0], 2187);
- /* "pysam/csamtools.pyx":2187
+ /* "pysam/csamtools.pyx":2190
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
* cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
@@ -22192,7 +22936,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_t_1 = __pyx_v_src->core.l_qseq;
__pyx_v_end_offset = __pyx_t_1;
- /* "pysam/csamtools.pyx":2189
+ /* "pysam/csamtools.pyx":2192
* cdef uint32_t end_offset = src.core.l_qseq
*
* if src.core.n_cigar>1: # <<<<<<<<<<<<<<
@@ -22202,7 +22946,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_t_2 = (__pyx_v_src->core.n_cigar > 1);
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":2190
+ /* "pysam/csamtools.pyx":2193
*
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
@@ -22211,7 +22955,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2191
+ /* "pysam/csamtools.pyx":2194
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<<
@@ -22220,7 +22964,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
- /* "pysam/csamtools.pyx":2192
+ /* "pysam/csamtools.pyx":2195
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -22229,7 +22973,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2197
+ /* "pysam/csamtools.pyx":2200
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -22238,7 +22982,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2193
+ /* "pysam/csamtools.pyx":2196
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
@@ -22247,7 +22991,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
case 5:
- /* "pysam/csamtools.pyx":2194
+ /* "pysam/csamtools.pyx":2197
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -22263,16 +23007,16 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2195
+ /* "pysam/csamtools.pyx":2198
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
* return -1
* elif op==BAM_CSOFT_CLIP:
*/
- PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_144);
+ PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_143);
- /* "pysam/csamtools.pyx":2196
+ /* "pysam/csamtools.pyx":2199
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
@@ -22286,7 +23030,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2197
+ /* "pysam/csamtools.pyx":2200
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -22295,7 +23039,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
case 4:
- /* "pysam/csamtools.pyx":2198
+ /* "pysam/csamtools.pyx":2201
* return -1
* elif op==BAM_CSOFT_CLIP:
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
@@ -22306,7 +23050,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
break;
default:
- /* "pysam/csamtools.pyx":2200
+ /* "pysam/csamtools.pyx":2203
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
@@ -22322,7 +23066,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2202
+ /* "pysam/csamtools.pyx":2205
* break
*
* if end_offset==0: # <<<<<<<<<<<<<<
@@ -22332,7 +23076,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_t_4 = (__pyx_v_end_offset == 0);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2203
+ /* "pysam/csamtools.pyx":2206
*
* if end_offset==0:
* end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
@@ -22345,7 +23089,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
}
__pyx_L7:;
- /* "pysam/csamtools.pyx":2205
+ /* "pysam/csamtools.pyx":2208
* end_offset = src.core.l_qseq
*
* return end_offset # <<<<<<<<<<<<<<
@@ -22362,7 +23106,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2208
+/* "pysam/csamtools.pyx":2211
*
*
* cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
@@ -22386,9 +23130,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("get_seq_range", 0);
- __Pyx_TraceCall("get_seq_range", __pyx_f[0], 2208);
+ __Pyx_TraceCall("get_seq_range", __pyx_f[0], 2211);
- /* "pysam/csamtools.pyx":2213
+ /* "pysam/csamtools.pyx":2216
* cdef char * s
*
* if not src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -22398,7 +23142,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
__pyx_t_1 = (!__pyx_v_src->core.l_qseq);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2214
+ /* "pysam/csamtools.pyx":2217
*
* if not src.core.l_qseq:
* return None # <<<<<<<<<<<<<<
@@ -22413,29 +23157,29 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2216
+ /* "pysam/csamtools.pyx":2219
* return None
*
* seq = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
* s = <char*>seq
* p = bam1_seq(src)
*/
- __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2217
+ /* "pysam/csamtools.pyx":2220
*
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq # <<<<<<<<<<<<<<
* p = bam1_seq(src)
*
*/
- __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_s = ((char *)__pyx_t_3);
- /* "pysam/csamtools.pyx":2218
+ /* "pysam/csamtools.pyx":2221
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq
* p = bam1_seq(src) # <<<<<<<<<<<<<<
@@ -22444,7 +23188,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "pysam/csamtools.pyx":2220
+ /* "pysam/csamtools.pyx":2223
* p = bam1_seq(src)
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
@@ -22454,7 +23198,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2223
+ /* "pysam/csamtools.pyx":2226
* # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
* # note: do not use string literal as it will be a python string
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] # <<<<<<<<<<<<<<
@@ -22464,7 +23208,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
(__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_5pysam_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
}
- /* "pysam/csamtools.pyx":2225
+ /* "pysam/csamtools.pyx":2228
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf]
*
* return seq # <<<<<<<<<<<<<<
@@ -22490,7 +23234,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2228
+/* "pysam/csamtools.pyx":2231
*
*
* cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
@@ -22514,9 +23258,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("get_qual_range", 0);
- __Pyx_TraceCall("get_qual_range", __pyx_f[0], 2228);
+ __Pyx_TraceCall("get_qual_range", __pyx_f[0], 2231);
- /* "pysam/csamtools.pyx":2233
+ /* "pysam/csamtools.pyx":2236
* cdef char * q
*
* p = bam1_qual(src) # <<<<<<<<<<<<<<
@@ -22525,7 +23269,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "pysam/csamtools.pyx":2234
+ /* "pysam/csamtools.pyx":2237
*
* p = bam1_qual(src)
* if p[0] == 0xff: # <<<<<<<<<<<<<<
@@ -22535,7 +23279,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
__pyx_t_1 = ((__pyx_v_p[0]) == 0xff);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2235
+ /* "pysam/csamtools.pyx":2238
* p = bam1_qual(src)
* if p[0] == 0xff:
* return None # <<<<<<<<<<<<<<
@@ -22550,29 +23294,29 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2237
+ /* "pysam/csamtools.pyx":2240
* return None
*
* qual = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
* q = <char*>qual
*
*/
- __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_qual = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2238
+ /* "pysam/csamtools.pyx":2241
*
* qual = PyBytes_FromStringAndSize(NULL, end - start)
* q = <char*>qual # <<<<<<<<<<<<<<
*
* for k from start <= k < end:
*/
- __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2238; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_q = ((char *)__pyx_t_3);
- /* "pysam/csamtools.pyx":2240
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* q = <char*>qual
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
@@ -22582,7 +23326,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2242
+ /* "pysam/csamtools.pyx":2245
* for k from start <= k < end:
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@@ -22592,7 +23336,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
(__pyx_v_q[(__pyx_v_k - __pyx_v_start)]) = ((__pyx_v_p[__pyx_v_k]) + 33);
}
- /* "pysam/csamtools.pyx":2244
+ /* "pysam/csamtools.pyx":2247
* q[k-start] = p[k] + 33
*
* return qual # <<<<<<<<<<<<<<
@@ -22632,7 +23376,7 @@ static int __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2276
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*
* # Now only called when instances are created from Python
* def __init__(self): # <<<<<<<<<<<<<<
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__init__", 0);
- __Pyx_TraceCall("__init__", __pyx_f[0], 2276);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 2279);
- /* "pysam/csamtools.pyx":2278
+ /* "pysam/csamtools.pyx":2281
* def __init__(self):
* # see bam_init1
* self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
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*/
__pyx_v_self->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "pysam/csamtools.pyx":2282
+ /* "pysam/csamtools.pyx":2285
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*/
__pyx_v_p = bam1_qname(__pyx_v_src);
- /* "pysam/csamtools.pyx":2388
+ /* "pysam/csamtools.pyx":2391
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*
* strncpy( p, qname, l ) # <<<<<<<<<<<<<<
*
* property cigar:
*/
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+ __pyx_t_7 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
strncpy(__pyx_v_p, __pyx_t_7, __pyx_v_l);
__pyx_r = 0;
@@ -23514,7 +24258,7 @@ static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(PyObje
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2423
+/* "pysam/csamtools.pyx":2426
*
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -23541,9 +24285,9 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2423);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2426);
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+ /* "pysam/csamtools.pyx":2432
* cdef int k
*
* src = self._delegate # <<<<<<<<<<<<<<
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
- /* "pysam/csamtools.pyx":2430
+ /* "pysam/csamtools.pyx":2433
*
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}
__pyx_L3:;
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*
* cigar = [] # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src);
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*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2435; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_cigar = ((PyObject *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":2433
+ /* "pysam/csamtools.pyx":2436
*
* cigar = []
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
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*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2434
+ /* "pysam/csamtools.pyx":2437
* cigar = []
* cigar_p = bam1_cigar(src);
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for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2435
+ /* "pysam/csamtools.pyx":2438
* cigar_p = bam1_cigar(src);
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*/
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+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF(__pyx_v_op);
__pyx_v_op = __pyx_t_3;
__pyx_t_3 = 0;
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+ /* "pysam/csamtools.pyx":2439
* for k from 0 <= k < src.core.n_cigar:
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+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF(__pyx_v_l);
__pyx_v_l = __pyx_t_3;
__pyx_t_3 = 0;
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* op = cigar_p[k] & BAM_CIGAR_MASK
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*/
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_op);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_op);
@@ -23642,13 +24386,13 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct
__Pyx_INCREF(__pyx_v_l);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_l);
__Pyx_GIVEREF(__pyx_v_l);
- __pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
- /* "pysam/csamtools.pyx":2438
+ /* "pysam/csamtools.pyx":2441
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l))
* return cigar # <<<<<<<<<<<<<<
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2440
+/* "pysam/csamtools.pyx":2443
* return cigar
*
* def __set__(self, values ): # <<<<<<<<<<<<<<
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__set__", 0);
- __Pyx_TraceCall("__set__", __pyx_f[0], 2440);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2443);
- /* "pysam/csamtools.pyx":2441
+ /* "pysam/csamtools.pyx":2444
*
* def __set__(self, values ):
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- __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
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+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
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@@ -23748,7 +24492,7 @@ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx
}
__pyx_L3:;
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+ /* "pysam/csamtools.pyx":2450
* cdef int k
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*/
__pyx_v_k = 0;
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+ /* "pysam/csamtools.pyx":2452
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__pyx_t_6 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_6;
- /* "pysam/csamtools.pyx":2452
+ /* "pysam/csamtools.pyx":2455
*
* # get location of cigar string
* p = bam1_cigar(src) # <<<<<<<<<<<<<<
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*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2457
+ /* "pysam/csamtools.pyx":2460
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+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2458
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* src.core.n_cigar * 4,
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*/
pysam_bam_update(__pyx_v_src, (__pyx_v_src->core.n_cigar * 4), (__pyx_t_3 * 4), ((uint8_t *)__pyx_v_p));
- /* "pysam/csamtools.pyx":2461
+ /* "pysam/csamtools.pyx":2464
*
* # length is number of cigar operations, not bytes
* src.core.n_cigar = len(values) # <<<<<<<<<<<<<<
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*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_src->core.n_cigar = __pyx_t_3;
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+ /* "pysam/csamtools.pyx":2468
* # re-acquire pointer to location in memory
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*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
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}
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return __pyx_r;
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__Pyx_RefNannySetupContext("__get__", 0);
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__pyx_t_1 = 0;
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__Pyx_XDECREF(__pyx_r);
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goto __pyx_L3;
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} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
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if (size > 2) __Pyx_RaiseTooManyValuesError(2);
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+ __pyx_t_4 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
if (__pyx_t_6) {
- /* "pysam/csamtools.pyx":2609
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@@ -24964,7 +25708,7 @@ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_
*/
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}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2611
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+ __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_qual)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_qual);
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
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+ __pyx_t_7 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_6 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
if (__pyx_t_6) {
- /* "pysam/csamtools.pyx":2617
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__Pyx_GIVEREF(__pyx_t_2);
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PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
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__pyx_L4:;
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* if src.core.l_qseq != l:
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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- /* "pysam/csamtools.pyx":2619
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for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_10; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2620
+ /* "pysam/csamtools.pyx":2623
* assert src.core.l_qseq == l
* for k from 0 <= k < l:
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return __pyx_r;
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__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2634);
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
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*/
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+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_start = __pyx_t_3;
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+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_end = __pyx_t_3;
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__Pyx_RefNannySetupContext("__get__", 0);
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__pyx_v_src = __pyx_t_1;
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__pyx_v_start = __pyx_t_3;
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+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_end = __pyx_t_3;
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return __pyx_r;
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2672);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2679);
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* def __get__(self):
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* property qlen:
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+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2677
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* property qlen:
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@@ -25476,9 +26220,9 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct _
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2677);
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+ /* "pysam/csamtools.pyx":2686
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
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* cdef bam1_t * src
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+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
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return __pyx_r;
}
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+/* "pysam/csamtools.pyx":2704
* multiple times.
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2697);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2704);
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+ /* "pysam/csamtools.pyx":2713
* cdef int32_t nvalues
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* src = self._delegate # <<<<<<<<<<<<<<
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
- /* "pysam/csamtools.pyx":2707
+ /* "pysam/csamtools.pyx":2714
*
* src = self._delegate
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__pyx_t_2 = (__pyx_v_src->l_aux == 0);
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_r = ((PyObject *)__pyx_t_3);
__pyx_t_3 = 0;
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__pyx_L3:;
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*/
__pyx_v_s = bam1_aux(__pyx_v_src);
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+ /* "pysam/csamtools.pyx":2716
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__pyx_v_result = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
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* s = bam1_aux( src )
* result = []
* auxtag[2] = 0 # <<<<<<<<<<<<<<
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*/
(__pyx_v_auxtag[2]) = 0;
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* result = []
* auxtag[2] = 0
* while s < (src.data + src.data_len): # <<<<<<<<<<<<<<
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__pyx_t_2 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
if (!__pyx_t_2) break;
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+ /* "pysam/csamtools.pyx":2720
* while s < (src.data + src.data_len):
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* auxtag[0] = s[0] # <<<<<<<<<<<<<<
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*/
(__pyx_v_auxtag[0]) = (__pyx_v_s[0]);
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+ /* "pysam/csamtools.pyx":2721
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*/
(__pyx_v_auxtag[1]) = (__pyx_v_s[1]);
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* auxtag[0] = s[0]
* auxtag[1] = s[1]
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*/
__pyx_v_s = (__pyx_v_s + 2);
- /* "pysam/csamtools.pyx":2716
+ /* "pysam/csamtools.pyx":2723
* auxtag[1] = s[1]
* s += 2
* auxtype = s[0] # <<<<<<<<<<<<<<
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*/
__pyx_v_auxtype = (__pyx_v_s[0]);
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__pyx_t_2 = __pyx_t_6;
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":2718
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__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
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goto __pyx_L6;
}
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__pyx_t_2 = __pyx_t_5;
if (__pyx_t_2) {
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__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
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goto __pyx_L6;
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__pyx_t_2 = __pyx_t_6;
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__Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
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goto __pyx_L6;
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goto __pyx_L6;
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goto __pyx_L6;
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goto __pyx_L6;
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@@ -30607,7 +31351,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15inferred_length___ge
case 1:
case 4:
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*
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}
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return __pyx_r;
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__pyx_v_src = __pyx_t_1;
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if (__pyx_t_5) {
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goto __pyx_L4;
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}
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+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3449; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
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PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
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__Pyx_GOTREF(__pyx_t_20);
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__Pyx_INCREF(__pyx_t_20);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_20);
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__Pyx_GIVEREF(__pyx_t_20);
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}
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
pysam_unset_stderr();
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+ /* "pysam/csamtools.pyx":3460
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__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
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+ /* "pysam/csamtools.pyx":3461
* pysam_unset_stderr()
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stderr_f);
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PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
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__pyx_v_inf = __pyx_t_4;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ /* "pysam/csamtools.pyx":3462
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+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3462; __pyx_clineno = __LINE__; goto __pyx_L92_error;}
__Pyx_GOTREF(__pyx_t_4);
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+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3462; __pyx_clineno = __LINE__; goto __pyx_L92_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":3454
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PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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}
/*else*/ {
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_196));
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return __pyx_r;
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+ __pyx_t_4 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4076; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L3:;
@@ -36920,7 +37666,7 @@ static void __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(PyObject *__p
__Pyx_RefNannyFinishContext();
}
-/* "pysam/csamtools.pyx":4078
+/* "pysam/csamtools.pyx":4085
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*
* def __dealloc__(self): # <<<<<<<<<<<<<<
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__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 4078);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 4085);
- /* "pysam/csamtools.pyx":4079
+ /* "pysam/csamtools.pyx":4086
*
* def __dealloc__(self):
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
@@ -36958,6 +37704,10 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastafile(PyTypeObject *t, PyObj
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p = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)o);
p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Fastafile;
+ p->_filename = Py_None; Py_INCREF(Py_None);
+ p->_references = Py_None; Py_INCREF(Py_None);
+ p->_lengths = Py_None; Py_INCREF(Py_None);
+ p->reference2length = Py_None; Py_INCREF(Py_None);
if (__pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
@@ -36965,6 +37715,8 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastafile(PyTypeObject *t, PyObj
}
static void __pyx_tp_dealloc_5pysam_9csamtools_Fastafile(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_Fastafile *p = (struct __pyx_obj_5pysam_9csamtools_Fastafile *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -36974,23 +37726,87 @@ static void __pyx_tp_dealloc_5pysam_9csamtools_Fastafile(PyObject *o) {
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
+ Py_CLEAR(p->_filename);
+ Py_CLEAR(p->_references);
+ Py_CLEAR(p->_lengths);
+ Py_CLEAR(p->reference2length);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
+static int __pyx_tp_traverse_5pysam_9csamtools_Fastafile(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools_Fastafile *p = (struct __pyx_obj_5pysam_9csamtools_Fastafile *)o;
+ if (p->_filename) {
+ e = (*v)(p->_filename, a); if (e) return e;
+ }
+ if (p->_references) {
+ e = (*v)(p->_references, a); if (e) return e;
+ }
+ if (p->_lengths) {
+ e = (*v)(p->_lengths, a); if (e) return e;
+ }
+ if (p->reference2length) {
+ e = (*v)(p->reference2length, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools_Fastafile(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_Fastafile *p = (struct __pyx_obj_5pysam_9csamtools_Fastafile *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->_filename);
+ p->_filename = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->_references);
+ p->_references = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->_lengths);
+ p->_lengths = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->reference2length);
+ p->reference2length = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *__pyx_sq_item_5pysam_9csamtools_Fastafile(PyObject *o, Py_ssize_t i) {
+ PyObject *r;
+ PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
+ r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
+ Py_DECREF(x);
+ return r;
+}
+
static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastafile_filename(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(o);
}
+static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastafile_references(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_9Fastafile_10references_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastafile_nreferences(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_9Fastafile_11nreferences_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastafile_lengths(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_9Fastafile_7lengths_1__get__(o);
+}
+
static PyMethodDef __pyx_methods_5pysam_9csamtools_Fastafile[] = {
{__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_2_isOpen)},
{__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_6_open)},
{__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_8close)},
{__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_12fetch)},
+ {__Pyx_NAMESTR("getReferenceLength"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_15getReferenceLength, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_14getReferenceLength)},
{0, 0, 0, 0}
};
static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Fastafile[] = {
- {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_198), 0},
+ {(char *)"references", __pyx_getprop_5pysam_9csamtools_9Fastafile_references, 0, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_9Fastafile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_200), 0},
+ {(char *)"lengths", __pyx_getprop_5pysam_9csamtools_9Fastafile_lengths, 0, __Pyx_DOCSTR(__pyx_k_201), 0},
{0, 0, 0, 0, 0}
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__pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
- 0, /*sq_item*/
+ __pyx_sq_item_5pysam_9csamtools_Fastafile, /*sq_item*/
0, /*sq_slice*/
0, /*sq_ass_item*/
0, /*sq_ass_slice*/
- 0, /*sq_contains*/
+ __pyx_pw_5pysam_9csamtools_9Fastafile_19__contains__, /*sq_contains*/
0, /*sq_inplace_concat*/
0, /*sq_inplace_repeat*/
};
static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
__pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*mp_length*/
- 0, /*mp_subscript*/
+ __pyx_pw_5pysam_9csamtools_9Fastafile_17__getitem__, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
@@ -37116,10 +37932,10 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(filename)*\n\n A *FASTA* file. The file is automatically opened.\n\n The file expects an indexed fasta file.\n\n TODO:\n add automatic indexing.\n add function to get sequence names.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools_Fastafile, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_Fastafile, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
@@ -37347,6 +38163,7 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastqfile(PyTypeObject *t, PyObj
if (!o) return 0;
p = ((struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o);
p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Fastqfile;
+ p->_filename = Py_None; Py_INCREF(Py_None);
if (__pyx_pw_5pysam_9csamtools_9Fastqfile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
@@ -37354,6 +38171,8 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastqfile(PyTypeObject *t, PyObj
}
static void __pyx_tp_dealloc_5pysam_9csamtools_Fastqfile(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_Fastqfile *p = (struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -37363,9 +38182,29 @@ static void __pyx_tp_dealloc_5pysam_9csamtools_Fastqfile(PyObject *o) {
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
+ Py_CLEAR(p->_filename);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
+static int __pyx_tp_traverse_5pysam_9csamtools_Fastqfile(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools_Fastqfile *p = (struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o;
+ if (p->_filename) {
+ e = (*v)(p->_filename, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools_Fastqfile(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_Fastqfile *p = (struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->_filename);
+ p->_filename = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastqfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_9csamtools_9Fastqfile_8filename_1__get__(o);
}
@@ -37375,12 +38214,11 @@ static PyMethodDef __pyx_methods_5pysam_9csamtools_Fastqfile[] = {
{__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_5_open, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_4_open)},
{__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_7close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_6close)},
{__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_13__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_12__next__)},
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{0, 0, 0, 0}
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static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Fastqfile[] = {
- {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastqfile_filename, 0, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastqfile_filename, 0, __Pyx_DOCSTR(__pyx_k_198), 0},
{0, 0, 0, 0, 0}
};
@@ -37506,10 +38344,10 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Fastqfile = {
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_Fastqfile, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(filename)*\n\n A *FASTQ* file. The file is automatically opened.\n\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools_Fastqfile, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_Fastqfile, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
__pyx_pw_5pysam_9csamtools_9Fastqfile_11__iter__, /*tp_iter*/
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};
static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_AlignedRead[] = {
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- {(char *)"aligned_pairs", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
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+ {(char *)"cigarstring", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_204), 0},
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+ {(char *)"rname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_214), 0},
+ {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tid, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_215), 0},
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+ {(char *)"rnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_223), 0},
+ {(char *)"mpos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_224), 0},
+ {(char *)"pnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_225), 0},
+ {(char *)"isize", __pyx_getprop_5pysam_9csamtools_11AlignedRead_isize, __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_226), 0},
+ {(char *)"tlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_227), 0},
+ {(char *)"is_paired", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_228), 0},
+ {(char *)"is_proper_pair", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_229), 0},
+ {(char *)"is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_230), 0},
+ {(char *)"mate_is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_231), 0},
+ {(char *)"is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_232), 0},
+ {(char *)"mate_is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_233), 0},
+ {(char *)"is_read1", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"is_read2", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_235), 0},
+ {(char *)"is_secondary", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_236), 0},
+ {(char *)"is_qcfail", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_237), 0},
+ {(char *)"is_duplicate", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_238), 0},
+ {(char *)"positions", __pyx_getprop_5pysam_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
+ {(char *)"inferred_length", __pyx_getprop_5pysam_9csamtools_11AlignedRead_inferred_length, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
+ {(char *)"aligned_pairs", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
{0, 0, 0, 0, 0}
};
@@ -38220,6 +39058,7 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools_Samfile(PyTypeObject *t, PyObjec
if (!o) return 0;
p = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)o);
p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Samfile;
+ p->_filename = Py_None; Py_INCREF(Py_None);
if (__pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
@@ -38227,6 +39066,8 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools_Samfile(PyTypeObject *t, PyObjec
}
static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *p = (struct __pyx_obj_5pysam_9csamtools_Samfile *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -38236,9 +39077,29 @@ static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) {
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
+ Py_CLEAR(p->_filename);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
+static int __pyx_tp_traverse_5pysam_9csamtools_Samfile(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *p = (struct __pyx_obj_5pysam_9csamtools_Samfile *)o;
+ if (p->_filename) {
+ e = (*v)(p->_filename, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools_Samfile(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *p = (struct __pyx_obj_5pysam_9csamtools_Samfile *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->_filename);
+ p->_filename = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(o);
}
@@ -38295,9 +39156,9 @@ static PyMethodDef __pyx_methods_5pysam_9csamtools_Samfile[] = {
};
static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Samfile[] = {
- {(char *)"filename", __pyx_getprop_5pysam_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_199), 0},
- {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
- {(char *)"references", __pyx_getprop_5pysam_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
+ {(char *)"filename", __pyx_getprop_5pysam_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_198), 0},
+ {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_200), 0},
+ {(char *)"references", __pyx_getprop_5pysam_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_199), 0},
{(char *)"lengths", __pyx_getprop_5pysam_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
{(char *)"mapped", __pyx_getprop_5pysam_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
{(char *)"unmapped", __pyx_getprop_5pysam_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
@@ -38428,10 +39289,10 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,\n add_sq_text = False, check_header = True, check_sq = True )*\n\n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n\n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary\n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :te [...]
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools_Samfile, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_Samfile, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
__pyx_pw_5pysam_9csamtools_7Samfile_41__iter__, /*tp_iter*/
@@ -41014,7 +41875,417 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__genexpr = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__genexpr = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__genexpr = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct__genexpr = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_scope_struct__genexpr, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct__genexpr, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct__genexpr, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_scope_struct__genexpr, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o);
+ p->__pyx_v_x = 0;
+ p->__pyx_v_y = 0;
+ p->__pyx_t_0 = 0;
+ p->__pyx_t_1 = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_x);
+ Py_CLEAR(p->__pyx_v_y);
+ Py_CLEAR(p->__pyx_t_0);
+ Py_CLEAR(p->__pyx_t_1);
+ PyObject_GC_Track(o);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ if (p->__pyx_v_x) {
+ e = (*v)(p->__pyx_v_x, a); if (e) return e;
+ }
+ if (p->__pyx_v_y) {
+ e = (*v)(p->__pyx_v_y, a); if (e) return e;
+ }
+ if (p->__pyx_t_0) {
+ e = (*v)(p->__pyx_t_0, a); if (e) return e;
+ }
+ if (p->__pyx_t_1) {
+ e = (*v)(p->__pyx_t_1, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->__pyx_v_x);
+ p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_v_y);
+ p->__pyx_v_y = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_0);
+ p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_1);
+ p->__pyx_t_1 = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_1_genexpr = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_scope_struct_1_genexpr, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct_1_genexpr, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct_1_genexpr, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_2__open(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *)o);
+ p->__pyx_v_data = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_2__open(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_data);
+ PyObject_GC_Track(o);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_2__open(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *)o;
+ if (p->__pyx_v_data) {
+ e = (*v)(p->__pyx_v_data, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_2__open(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->__pyx_v_data);
+ p->__pyx_v_data = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_2__open[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_2__open = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_2__open = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -41027,13 +42298,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__genexpr = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct__genexpr = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_2__open = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_2__open = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -41054,12 +42325,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_2__open = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_2__open"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_2__open, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -41069,24 +42340,24 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number___pyx_scope_struct__genexpr, /*tp_as_number*/
- &__pyx_tp_as_sequence___pyx_scope_struct__genexpr, /*tp_as_sequence*/
- &__pyx_tp_as_mapping___pyx_scope_struct__genexpr, /*tp_as_mapping*/
+ &__pyx_tp_as_number___pyx_scope_struct_2__open, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct_2__open, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct_2__open, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer___pyx_scope_struct__genexpr, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer___pyx_scope_struct_2__open, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_2__open, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_2__open, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct_2__open, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -41096,7 +42367,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_2__open, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -41110,70 +42381,271 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p;
+static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_3_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o);
+ p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *)o);
+ p->__pyx_outer_scope = 0;
p->__pyx_v_x = 0;
- p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
- p->__pyx_t_1 = 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_3_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *)o;
PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_outer_scope);
Py_CLEAR(p->__pyx_v_x);
- Py_CLEAR(p->__pyx_v_y);
Py_CLEAR(p->__pyx_t_0);
- Py_CLEAR(p->__pyx_t_1);
PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_3_genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *)o;
+ if (p->__pyx_outer_scope) {
+ e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+ }
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
- if (p->__pyx_v_y) {
- e = (*v)(p->__pyx_v_y, a); if (e) return e;
- }
if (p->__pyx_t_0) {
e = (*v)(p->__pyx_t_0, a); if (e) return e;
}
- if (p->__pyx_t_1) {
- e = (*v)(p->__pyx_t_1, a); if (e) return e;
- }
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_3_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr *)o;
PyObject* tmp;
+ tmp = ((PyObject*)p->__pyx_outer_scope);
+ p->__pyx_outer_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
- tmp = ((PyObject*)p->__pyx_v_y);
- p->__pyx_v_y = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
tmp = ((PyObject*)p->__pyx_t_0);
p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
- tmp = ((PyObject*)p->__pyx_t_1);
- p->__pyx_t_1 = Py_None; Py_INCREF(Py_None);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_3_genexpr[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_3_genexpr = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_3_genexpr = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_3_genexpr = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_3_genexpr = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_3_genexpr = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_3_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_3_genexpr, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_scope_struct_3_genexpr, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct_3_genexpr, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct_3_genexpr, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_scope_struct_3_genexpr, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_3_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_3_genexpr, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct_3_genexpr, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_3_genexpr, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_4_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *)o);
+ p->__pyx_outer_scope = 0;
+ p->__pyx_v_x = 0;
+ p->__pyx_t_0 = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_4_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_outer_scope);
+ Py_CLEAR(p->__pyx_v_x);
+ Py_CLEAR(p->__pyx_t_0);
+ PyObject_GC_Track(o);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_4_genexpr(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *)o;
+ if (p->__pyx_outer_scope) {
+ e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+ }
+ if (p->__pyx_v_x) {
+ e = (*v)(p->__pyx_v_x, a); if (e) return e;
+ }
+ if (p->__pyx_t_0) {
+ e = (*v)(p->__pyx_t_0, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_4_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->__pyx_outer_scope);
+ p->__pyx_outer_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_v_x);
+ p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->__pyx_t_0);
+ p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr[] = {
+static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_4_genexpr[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_4_genexpr = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -41231,7 +42703,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_4_genexpr = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -41244,13 +42716,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_1_genexpr = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_4_genexpr = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_4_genexpr = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -41271,12 +42743,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr = {
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_4_genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_4_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_4_genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -41286,24 +42758,24 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr =
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number___pyx_scope_struct_1_genexpr, /*tp_as_number*/
- &__pyx_tp_as_sequence___pyx_scope_struct_1_genexpr, /*tp_as_sequence*/
- &__pyx_tp_as_mapping___pyx_scope_struct_1_genexpr, /*tp_as_mapping*/
+ &__pyx_tp_as_number___pyx_scope_struct_4_genexpr, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_scope_struct_4_genexpr, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_scope_struct_4_genexpr, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer___pyx_scope_struct_4_genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_4_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_4_genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct_4_genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -41313,7 +42785,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr =
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_4_genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -41351,39 +42823,37 @@ static struct PyModuleDef __pyx_moduledef = {
static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_u_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 1, 0, 0},
- {&__pyx_kp_s_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 1, 0},
- {&__pyx_kp_s_100, __pyx_k_100, sizeof(__pyx_k_100), 0, 0, 1, 0},
- {&__pyx_kp_s_102, __pyx_k_102, sizeof(__pyx_k_102), 0, 0, 1, 0},
- {&__pyx_kp_s_105, __pyx_k_105, sizeof(__pyx_k_105), 0, 0, 1, 0},
- {&__pyx_kp_s_110, __pyx_k_110, sizeof(__pyx_k_110), 0, 0, 1, 0},
- {&__pyx_kp_s_112, __pyx_k_112, sizeof(__pyx_k_112), 0, 0, 1, 0},
+ {&__pyx_kp_b_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 0, 0},
+ {&__pyx_kp_s_101, __pyx_k_101, sizeof(__pyx_k_101), 0, 0, 1, 0},
+ {&__pyx_kp_s_104, __pyx_k_104, sizeof(__pyx_k_104), 0, 0, 1, 0},
+ {&__pyx_kp_s_109, __pyx_k_109, sizeof(__pyx_k_109), 0, 0, 1, 0},
+ {&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0},
+ {&__pyx_kp_s_111, __pyx_k_111, sizeof(__pyx_k_111), 0, 0, 1, 0},
+ {&__pyx_kp_s_113, __pyx_k_113, sizeof(__pyx_k_113), 0, 0, 1, 0},
{&__pyx_kp_s_114, __pyx_k_114, sizeof(__pyx_k_114), 0, 0, 1, 0},
{&__pyx_kp_s_115, __pyx_k_115, sizeof(__pyx_k_115), 0, 0, 1, 0},
- {&__pyx_kp_s_116, __pyx_k_116, sizeof(__pyx_k_116), 0, 0, 1, 0},
+ {&__pyx_kp_s_118, __pyx_k_118, sizeof(__pyx_k_118), 0, 0, 1, 0},
{&__pyx_kp_s_119, __pyx_k_119, sizeof(__pyx_k_119), 0, 0, 1, 0},
{&__pyx_kp_s_120, __pyx_k_120, sizeof(__pyx_k_120), 0, 0, 1, 0},
{&__pyx_kp_s_121, __pyx_k_121, sizeof(__pyx_k_121), 0, 0, 1, 0},
{&__pyx_kp_s_122, __pyx_k_122, sizeof(__pyx_k_122), 0, 0, 1, 0},
- {&__pyx_kp_s_123, __pyx_k_123, sizeof(__pyx_k_123), 0, 0, 1, 0},
- {&__pyx_kp_s_125, __pyx_k_125, sizeof(__pyx_k_125), 0, 0, 1, 0},
- {&__pyx_kp_s_128, __pyx_k_128, sizeof(__pyx_k_128), 0, 0, 1, 0},
- {&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
- {&__pyx_kp_s_131, __pyx_k_131, sizeof(__pyx_k_131), 0, 0, 1, 0},
+ {&__pyx_kp_s_124, __pyx_k_124, sizeof(__pyx_k_124), 0, 0, 1, 0},
+ {&__pyx_kp_s_127, __pyx_k_127, sizeof(__pyx_k_127), 0, 0, 1, 0},
+ {&__pyx_kp_s_130, __pyx_k_130, sizeof(__pyx_k_130), 0, 0, 1, 0},
+ {&__pyx_kp_s_136, __pyx_k_136, sizeof(__pyx_k_136), 0, 0, 1, 0},
{&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0},
{&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0},
- {&__pyx_kp_s_139, __pyx_k_139, sizeof(__pyx_k_139), 0, 0, 1, 0},
- {&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0},
+ {&__pyx_kp_s_140, __pyx_k_140, sizeof(__pyx_k_140), 0, 0, 1, 0},
+ {&__pyx_kp_s_146, __pyx_k_146, sizeof(__pyx_k_146), 0, 0, 1, 0},
{&__pyx_kp_s_147, __pyx_k_147, sizeof(__pyx_k_147), 0, 0, 1, 0},
{&__pyx_kp_s_148, __pyx_k_148, sizeof(__pyx_k_148), 0, 0, 1, 0},
{&__pyx_kp_s_149, __pyx_k_149, sizeof(__pyx_k_149), 0, 0, 1, 0},
{&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
- {&__pyx_kp_s_150, __pyx_k_150, sizeof(__pyx_k_150), 0, 0, 1, 0},
+ {&__pyx_kp_s_151, __pyx_k_151, sizeof(__pyx_k_151), 0, 0, 1, 0},
{&__pyx_kp_s_152, __pyx_k_152, sizeof(__pyx_k_152), 0, 0, 1, 0},
- {&__pyx_kp_s_153, __pyx_k_153, sizeof(__pyx_k_153), 0, 0, 1, 0},
- {&__pyx_kp_s_157, __pyx_k_157, sizeof(__pyx_k_157), 0, 0, 1, 0},
- {&__pyx_n_s_159, __pyx_k_159, sizeof(__pyx_k_159), 0, 0, 1, 1},
- {&__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_156, __pyx_k_156, sizeof(__pyx_k_156), 0, 0, 1, 0},
+ {&__pyx_n_s_158, __pyx_k_158, sizeof(__pyx_k_158), 0, 0, 1, 1},
+ {&__pyx_kp_s_159, __pyx_k_159, sizeof(__pyx_k_159), 0, 0, 1, 0},
{&__pyx_kp_s_160, __pyx_k_160, sizeof(__pyx_k_160), 0, 0, 1, 0},
{&__pyx_kp_s_161, __pyx_k_161, sizeof(__pyx_k_161), 0, 0, 1, 0},
{&__pyx_kp_s_162, __pyx_k_162, sizeof(__pyx_k_162), 0, 0, 1, 0},
@@ -41405,19 +42875,22 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
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{&__pyx_kp_s_178, __pyx_k_178, sizeof(__pyx_k_178), 0, 0, 1, 0},
{&__pyx_kp_s_179, __pyx_k_179, sizeof(__pyx_k_179), 0, 0, 1, 0},
- {&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
{&__pyx_kp_s_180, __pyx_k_180, sizeof(__pyx_k_180), 0, 0, 1, 0},
{&__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},
- {&__pyx_kp_s_185, __pyx_k_185, sizeof(__pyx_k_185), 0, 0, 1, 0},
+ {&__pyx_kp_s_184, __pyx_k_184, sizeof(__pyx_k_184), 0, 0, 1, 0},
+ {&__pyx_kp_s_188, __pyx_k_188, sizeof(__pyx_k_188), 0, 0, 1, 0},
{&__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},
- {&__pyx_kp_s_191, __pyx_k_191, sizeof(__pyx_k_191), 0, 0, 1, 0},
+ {&__pyx_kp_s_196, __pyx_k_196, sizeof(__pyx_k_196), 0, 0, 1, 0},
{&__pyx_kp_s_197, __pyx_k_197, sizeof(__pyx_k_197), 0, 0, 1, 0},
- {&__pyx_kp_s_198, __pyx_k_198, sizeof(__pyx_k_198), 0, 0, 1, 0},
+ {&__pyx_kp_b_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 0, 0},
+ {&__pyx_kp_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 0},
{&__pyx_kp_s_21, __pyx_k_21, sizeof(__pyx_k_21), 0, 0, 1, 0},
+ {&__pyx_kp_s_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 1, 0},
+ {&__pyx_kp_s_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 1, 0},
+ {&__pyx_kp_s_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 1, 0},
{&__pyx_n_s_262, __pyx_k_262, sizeof(__pyx_k_262), 0, 0, 1, 1},
{&__pyx_kp_s_264, __pyx_k_264, sizeof(__pyx_k_264), 0, 0, 1, 0},
{&__pyx_kp_s_269, __pyx_k_269, sizeof(__pyx_k_269), 0, 0, 1, 0},
@@ -41434,13 +42907,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_294, __pyx_k_294, sizeof(__pyx_k_294), 0, 0, 1, 1},
{&__pyx_kp_s_295, __pyx_k_295, sizeof(__pyx_k_295), 0, 0, 1, 0},
{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
+ {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
{&__pyx_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},
{&__pyx_n_s_310, __pyx_k_310, sizeof(__pyx_k_310), 0, 0, 1, 1},
{&__pyx_n_s_313, __pyx_k_313, sizeof(__pyx_k_313), 0, 0, 1, 1},
{&__pyx_n_s_316, __pyx_k_316, sizeof(__pyx_k_316), 0, 0, 1, 1},
{&__pyx_kp_s_317, __pyx_k_317, sizeof(__pyx_k_317), 0, 0, 1, 0},
- {&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
+ {&__pyx_kp_b_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 0, 0},
+ {&__pyx_kp_b_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 0, 0},
+ {&__pyx_kp_b_35, __pyx_k_35, sizeof(__pyx_k_35), 0, 0, 0, 0},
{&__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},
@@ -41474,6 +42950,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_kp_s_90, __pyx_k_90, sizeof(__pyx_k_90), 0, 0, 1, 0},
{&__pyx_kp_s_93, __pyx_k_93, sizeof(__pyx_k_93), 0, 0, 1, 0},
+ {&__pyx_kp_s_99, __pyx_k_99, sizeof(__pyx_k_99), 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},
@@ -41507,6 +42984,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__ID, __pyx_k__ID, sizeof(__pyx_k__ID), 0, 0, 1, 1},
{&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
{&__pyx_n_s__IS_PYTHON3, __pyx_k__IS_PYTHON3, sizeof(__pyx_k__IS_PYTHON3), 0, 0, 1, 1},
+ {&__pyx_n_s__IndexError, __pyx_k__IndexError, sizeof(__pyx_k__IndexError), 0, 0, 1, 1},
{&__pyx_n_s__IndexedReads, __pyx_k__IndexedReads, sizeof(__pyx_k__IndexedReads), 0, 0, 1, 1},
{&__pyx_n_s__IteratorColumn, __pyx_k__IteratorColumn, sizeof(__pyx_k__IteratorColumn), 0, 0, 1, 1},
{&__pyx_n_s__IteratorRow, __pyx_k__IteratorRow, sizeof(__pyx_k__IteratorRow), 0, 0, 1, 1},
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- __pyx_k_tuple_33 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_33);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33));
+ __pyx_k_tuple_31 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_31);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_31));
- /* "pysam/csamtools.pyx":917
+ /* "pysam/csamtools.pyx":803
+ * self.isbam = len(mode) > 1 and mode[1] == 'b'
+ *
+ * self.isremote = filename.startswith(b"http:") or filename.startswith(b"ftp:") # <<<<<<<<<<<<<<
+ *
+ * cdef char * ctext
+ */
+ __pyx_k_tuple_34 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_b_33)); if (unlikely(!__pyx_k_tuple_34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_34);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_34));
+ __pyx_k_tuple_36 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_b_35)); if (unlikely(!__pyx_k_tuple_36)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_36);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_36));
+
+ /* "pysam/csamtools.pyx":922
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* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference )
*/
- __pyx_k_tuple_47 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_47 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_47);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
- /* "pysam/csamtools.pyx":924
+ /* "pysam/csamtools.pyx":929
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_k_tuple_48 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_48 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_48);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48));
- /* "pysam/csamtools.pyx":932
+ /* "pysam/csamtools.pyx":937
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
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+ __pyx_k_tuple_50 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_50);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_50));
- /* "pysam/csamtools.pyx":982
+ /* "pysam/csamtools.pyx":987
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*
* if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
*
* rtid = self.gettid( reference )
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+ __pyx_k_tuple_52 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_0, __pyx_int_0, __pyx_int_0); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_52);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
- /* "pysam/csamtools.pyx":1002
+ /* "pysam/csamtools.pyx":1007
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
*/
- __pyx_k_tuple_55 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_55 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_55);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
- /* "pysam/csamtools.pyx":1004
+ /* "pysam/csamtools.pyx":1009
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
* if self.isstream:
* raise OSError("seek no available in streams")
*/
- __pyx_k_tuple_57 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_57 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_57);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
- /* "pysam/csamtools.pyx":1006
+ /* "pysam/csamtools.pyx":1011
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
* raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
*
* return bam_seek( self.samfile.x.bam, offset, where )
*/
- __pyx_k_tuple_59 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_58)); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_59 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_58)); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_59);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));
- /* "pysam/csamtools.pyx":1015
+ /* "pysam/csamtools.pyx":1020
* '''
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
*/
- __pyx_k_tuple_60 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_60 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_60);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_60));
- /* "pysam/csamtools.pyx":1017
+ /* "pysam/csamtools.pyx":1022
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
*
* return bam_tell( self.samfile.x.bam )
*/
- __pyx_k_tuple_61 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1017; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_61 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_61);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
- /* "pysam/csamtools.pyx":1052
+ /* "pysam/csamtools.pyx":1057
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
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+ __pyx_k_tuple_63 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_63);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
- /* "pysam/csamtools.pyx":1061
+ /* "pysam/csamtools.pyx":1066
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
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* if callback:
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+ __pyx_k_tuple_65 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_64)); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_65);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65));
- /* "pysam/csamtools.pyx":1064
+ /* "pysam/csamtools.pyx":1069
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
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+ __pyx_k_tuple_67 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_66)); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1069; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_67);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67));
- /* "pysam/csamtools.pyx":1065
+ /* "pysam/csamtools.pyx":1070
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
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*/
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+ __pyx_k_tuple_69 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_68)); if (unlikely(!__pyx_k_tuple_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_69);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_69));
- /* "pysam/csamtools.pyx":1085
+ /* "pysam/csamtools.pyx":1090
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* if has_coord:
* raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
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* if callback:
*/
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+ __pyx_k_tuple_71 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_70)); if (unlikely(!__pyx_k_tuple_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_71);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_71));
- /* "pysam/csamtools.pyx":1088
+ /* "pysam/csamtools.pyx":1093
*
* if callback:
* raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
*
* if self.samfile.header == NULL:
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+ __pyx_k_tuple_73 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_72)); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_73);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73));
- /* "pysam/csamtools.pyx":1091
+ /* "pysam/csamtools.pyx":1096
*
* if self.samfile.header == NULL:
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+ __pyx_k_tuple_75 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_74)); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_75);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
- /* "pysam/csamtools.pyx":1096
+ /* "pysam/csamtools.pyx":1101
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+ __pyx_k_tuple_76 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_74)); if (unlikely(!__pyx_k_tuple_76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_76);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_76));
- /* "pysam/csamtools.pyx":1137
+ /* "pysam/csamtools.pyx":1142
*
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+ __pyx_k_tuple_80 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_79)); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_80);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
- /* "pysam/csamtools.pyx":1162
+ /* "pysam/csamtools.pyx":1167
*
* if not self._isOpen():
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+ __pyx_k_tuple_82 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_82);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_82));
- /* "pysam/csamtools.pyx":1171
+ /* "pysam/csamtools.pyx":1176
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
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+ __pyx_k_tuple_83 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_64)); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_83);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83));
- /* "pysam/csamtools.pyx":1174
+ /* "pysam/csamtools.pyx":1179
*
* if not region:
* raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
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+ __pyx_k_tuple_85 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_84)); if (unlikely(!__pyx_k_tuple_85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_85);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_85));
- /* "pysam/csamtools.pyx":1175
+ /* "pysam/csamtools.pyx":1180
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* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
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+ __pyx_k_tuple_86 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_68)); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_86);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
- /* "pysam/csamtools.pyx":1185
+ /* "pysam/csamtools.pyx":1190
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* def pileup( self,
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+ __pyx_k_tuple_88 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_87)); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_88);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_88));
- /* "pysam/csamtools.pyx":1244
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* if not self._isOpen():
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+ __pyx_k_tuple_89 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_89);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89));
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+ /* "pysam/csamtools.pyx":1254
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__Pyx_GOTREF(__pyx_k_tuple_91);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_91));
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* if callback:
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__Pyx_GOTREF(__pyx_k_tuple_92);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_92));
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* else:
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__Pyx_GOTREF(__pyx_k_tuple_94);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_94));
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+ /* "pysam/csamtools.pyx":1326
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* def __get__(self):
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- __Pyx_GOTREF(__pyx_k_tuple_96);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
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* def __get__(self):
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
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* def __get__(self):
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
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* def __get__(self):
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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_99));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_101));
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* def __get__(self):
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_104));
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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_106));
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* '''full contents of the :term:`sam file` header as a string.'''
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* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
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* '''
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_108));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_111));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_113));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117));
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__Pyx_GOTREF(__pyx_k_tuple_265);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_265));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_296));
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__Pyx_GOTREF(__pyx_k_tuple_297);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_297));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_298));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_299));
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* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_300));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_301));
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+ __pyx_k_codeobj_302 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_301, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s____init__, 3343, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_302)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_k_tuple_303);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_303));
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+ __pyx_k_tuple_305 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filename), ((PyObject *)__pyx_n_s__fd)); if (unlikely(!__pyx_k_tuple_305)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_305));
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+ /* "pysam/csamtools.pyx":3352
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_311));
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@@ -43009,20 +44503,30 @@ PyMODINIT_FUNC PyInit_csamtools(void)
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__pyx_vtabptr_5pysam_9csamtools_Fastafile = &__pyx_vtable_5pysam_9csamtools_Fastafile;
__pyx_vtable_5pysam_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_5pysam_9csamtools_9Fastafile__fetch;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Fastafile, "__contains__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_5pysam_9csamtools_9Fastafile_18__contains__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_9Fastafile_18__contains__.doc = __pyx_doc_5pysam_9csamtools_9Fastafile_18__contains__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_9Fastafile_18__contains__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_Fastafile = &__pyx_type_5pysam_9csamtools_Fastafile;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_FastqProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "FastqProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_FastqProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_FastqProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "FastqProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_FastqProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_FastqProxy = &__pyx_type_5pysam_9csamtools_FastqProxy;
__pyx_vtabptr_5pysam_9csamtools_Fastqfile = &__pyx_vtable_5pysam_9csamtools_Fastqfile;
__pyx_vtable_5pysam_9csamtools_Fastqfile.getCurrent = (kseq_t *(*)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *))__pyx_f_5pysam_9csamtools_9Fastqfile_getCurrent;
__pyx_vtable_5pysam_9csamtools_Fastqfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *))__pyx_f_5pysam_9csamtools_9Fastqfile_cnext;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Fastqfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Fastqfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_9csamtools_9Fastqfile_12__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_9csamtools_9Fastqfile_12__next__.doc = __pyx_doc_5pysam_9csamtools_9Fastqfile_12__next__;
@@ -43030,13 +44534,13 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastqfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastqfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastqfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastqfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_Fastqfile = &__pyx_type_5pysam_9csamtools_Fastqfile;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_5pysam_9csamtools_11AlignedRead_4__str__;
@@ -43044,7 +44548,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_AlignedRead = &__pyx_type_5pysam_9csamtools_AlignedRead;
__pyx_vtabptr_5pysam_9csamtools_Samfile = &__pyx_vtable_5pysam_9csamtools_Samfile;
__pyx_vtable_5pysam_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *))__pyx_f_5pysam_9csamtools_7Samfile__buildHeader;
@@ -43052,10 +44556,10 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__pyx_vtable_5pysam_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_cnext;
__pyx_vtable_5pysam_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_5pysam_9csamtools_7Samfile_write;
__pyx_vtable_5pysam_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int))__pyx_f_5pysam_9csamtools_7Samfile__getrname;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __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 = 671; __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 = 684; __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__;
@@ -43063,26 +44567,26 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- 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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __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 = 684; __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 = 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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3253; __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 = 3253; __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 = 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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3305; __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 = 3305; __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 = 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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __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 = 1575; __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 = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1600; __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 = 1597; __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 = 1600; __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__;
@@ -43090,17 +44594,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- 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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1600; __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 = 1600; __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 = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __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 = 1681; __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 = 1684; __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__;
@@ -43108,14 +44612,14 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- 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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __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 = 1684; __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 = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __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 = 1745; __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 = 1748; __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__;
@@ -43123,16 +44627,16 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- 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;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __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 = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __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 = 1792; __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 = 1795; __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__;
@@ -43140,8 +44644,8 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- 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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __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 = 1795; __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;
@@ -43149,17 +44653,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__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 = 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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1924; __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 = 1924; __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 = 1924; __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 = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
@@ -43167,16 +44671,16 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = &__pyx_type_5pysam_9csamtools_IteratorColumnRegion;
__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
__pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__.doc = __pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
@@ -43184,19 +44688,25 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_IndexedReads = &__pyx_type_5pysam_9csamtools_IndexedReads;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools_SNPCall = &__pyx_type_5pysam_9csamtools_SNPCall;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_2__open) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools___pyx_scope_struct_2__open = &__pyx_type_5pysam_9csamtools___pyx_scope_struct_2__open;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_3_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools___pyx_scope_struct_3_genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct_3_genexpr;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_4_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools___pyx_scope_struct_4_genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct_4_genexpr;
/*--- Type import code ---*/
__pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
#if CYTHON_COMPILING_IN_PYPY
@@ -43438,7 +44948,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":138
+ /* "pysam/csamtools.pyx":137
* DEF BAM_CDIFF = 8
*
* cdef char* CODE2CIGAR= "MIDNSHP=X" # <<<<<<<<<<<<<<
@@ -43447,83 +44957,83 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*/
__pyx_v_5pysam_9csamtools_CODE2CIGAR = __pyx_k_263;
- /* "pysam/csamtools.pyx":139
+ /* "pysam/csamtools.pyx":138
*
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3: # <<<<<<<<<<<<<<
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
* else:
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__IS_PYTHON3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*
*/
- __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_k_188 = __pyx_t_4;
+ __pyx_k_187 = __pyx_t_4;
__Pyx_GIVEREF(__pyx_t_4);
__pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":3369
+ /* "pysam/csamtools.pyx":3376
* del self.streams[-1]
*
* def _samtools_dispatch( method, # <<<<<<<<<<<<<<
* args = (),
* catch_stdout = True ):
*/
- __pyx_t_4 = PyCFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s_271); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyCFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s_271); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/csamtools.pyx":4081
+ /* "pysam/csamtools.pyx":4088
* if self.owns_samfile: samclose( self.fp )
*
* __all__ = ["Samfile", # <<<<<<<<<<<<<<
* "Fastafile",
* "Fastqfile",
*/
- __pyx_t_4 = PyList_New(10); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4081; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_New(10); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile));
PyList_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_n_s__Samfile));
@@ -44176,7 +45686,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__Pyx_INCREF(((PyObject *)__pyx_n_s__IndexedReads));
PyList_SET_ITEM(__pyx_t_4, 9, ((PyObject *)__pyx_n_s__IndexedReads));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndexedReads));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4081; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
/* "pysam/csamtools.pyx":1
@@ -44560,6 +46070,67 @@ invalid_keyword:
return 0;
}
+static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
+ PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
+}
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ #endif
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ /* Make sure tstate is in a consistent state when we XDECREF
+ these objects (DECREF may run arbitrary code). */
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name,
PyObject* kw_name)
@@ -44719,63 +46290,6 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
return 0;
}
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
- if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- #endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
- return 0;
-bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
"too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index 8341814..ecd08ae 100644
--- a/pysam/csamtools.pxd
+++ b/pysam/csamtools.pxd
@@ -426,17 +426,15 @@ ctypedef struct __iterdata:
# Note: need to declare all C fields and methods here
#
cdef class Fastafile:
- cdef char * _filename
- # pointer to fastafile
- cdef faidx_t * fastafile
-
- cdef char * _fetch( self, char * reference, int start, int end, int * length )
+ cdef object _filename, _references, _lengths, reference2length
+ cdef faidx_t* fastafile
+ cdef char* _fetch(self, char* reference, int start, int end, int* length)
cdef class FastqProxy:
cdef kseq_t * _delegate
cdef class Fastqfile:
- cdef char * _filename
+ cdef object _filename
cdef gzFile fastqfile
cdef kseq_t * entry
@@ -449,7 +447,7 @@ cdef class AlignedRead:
cdef bam1_t * _delegate
cdef class Samfile:
- cdef char * _filename
+ cdef object _filename
# pointer to samfile
cdef samfile_t * samfile
# pointer to index
diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx
index 763798f..90033bd 100644
--- a/pysam/csamtools.pyx
+++ b/pysam/csamtools.pyx
@@ -38,9 +38,8 @@ if _FILENAME_ENCODING is None:
#cdef char* _C_FILENAME_ENCODING
#_C_FILENAME_ENCODING = <char*>_FILENAME_ENCODING
-cdef bytes _my_encodeFilename(object filename):
- u"""Make sure a filename is 8-bit encoded (or None).
- """
+cdef bytes _encodeFilename(object filename):
+ """Make sure a filename is 8-bit encoded (or None)."""
if filename is None:
return None
elif PyBytes_Check(filename):
@@ -393,7 +392,10 @@ cdef class Fastafile:
def __cinit__(self, *args, **kwargs ):
self.fastafile = NULL
- self._filename = NULL
+ self._filename = None
+ self._references = None
+ self._lengths = None
+ self.reference2length = None
self._open( *args, **kwargs )
def _isOpen( self ):
@@ -406,8 +408,7 @@ cdef class Fastafile:
return faidx_fetch_nseq(self.fastafile)
- def _open( self,
- filename ):
+ def _open(self, filename):
'''open an indexed fasta file.
This method expects an indexed fasta file.
@@ -415,13 +416,21 @@ cdef class Fastafile:
# close a previously opened file
if self.fastafile != NULL: self.close()
- if self._filename != NULL: free(self._filename)
- filename = _my_encodeFilename(filename)
- self._filename = strdup(filename)
- self.fastafile = fai_load( filename )
+ self._filename = _encodeFilename(filename)
+ self.fastafile = fai_load(self._filename)
if self.fastafile == NULL:
- raise IOError("could not open file `%s`" % filename )
+ raise IOError("could not open file `%s`" % filename)
+
+ # read index
+ if not os.path.exists( self._filename + b".fai" ):
+ raise ValueError("could not locate index file")
+
+ with open( self._filename + b".fai" ) as inf:
+ data = [ x.split("\t") for x in inf ]
+ self._references = tuple(x[0] for x in data)
+ self._lengths = tuple(int(x[1]) for x in data)
+ self.reference2length = dict(zip(self._references, self._lengths))
def close( self ):
if self.fastafile != NULL:
@@ -430,14 +439,27 @@ cdef class Fastafile:
def __dealloc__(self):
self.close()
- if self._filename != NULL: free(self._filename)
property filename:
'''number of :term:`filename` associated with this object.'''
def __get__(self):
- if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
return self._filename
+ property references:
+ '''tuple with the names of :term:`reference` sequences.'''
+ def __get__(self):
+ return self._references
+
+ property nreferences:
+ '''number of :term:`reference` sequences in the file.'''
+ def __get__(self):
+ return len(self._references) if self.references else None
+
+ property lengths:
+ '''tuple with the lengths of :term:`reference` sequences.'''
+ def __get__(self):
+ return self._lengths
+
def fetch( self,
reference = None,
start = None,
@@ -473,8 +495,8 @@ cdef class Fastafile:
if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
if start == end: return b""
# valid ranges are from 0 to 2^29-1
- if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
- if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end )
+ if not 0 <= start < max_pos: raise IndexError( 'start out of range (%i)' % start )
+ if not 0 <= end < max_pos: raise IndexError( 'end out of range (%i)' % end )
# note: faidx_fetch_seq has a bug such that out-of-range access
# always returns the last residue. Hence do not use faidx_fetch_seq,
# but use fai_fetch instead
@@ -513,6 +535,16 @@ cdef class Fastafile:
end-1,
length )
+ def getReferenceLength( self, reference ):
+ '''return the length of reference.'''
+ return self.reference2length[reference]
+
+ def __getitem__(self, reference):
+ return self.fetch(reference)
+
+ def __contains__( self, reference ):
+ '''return true if reference in fasta file.'''
+ return reference in self.reference2length
######################################################################
######################################################################
@@ -549,48 +581,45 @@ cdef class Fastqfile:
A *FASTQ* file. The file is automatically opened.
'''
-
def __cinit__(self, *args, **kwargs ):
- # self.fastqfile = NULL
- self._filename = NULL
+ # self.fastqfile = <gzFile*>NULL
+ self._filename = None
+ self.entry = NULL
self._open( *args, **kwargs )
def _isOpen( self ):
'''return true if samfile has been opened.'''
- return self._filename != NULL
+ return self.entry != NULL
- def _open( self,
- filename ):
+ def _open(self, filename):
'''open an indexed fasta file.
This method expects an indexed fasta file.
'''
+ self.close()
if not os.path.exists( filename ):
raise IOError( "No such file or directory: %s" % filename )
- # close a previously opened file
- # if self.fastqfile != NULL: self.close()
- if self._filename != NULL: free(self._filename)
- filename = _my_encodeFilename(filename)
- self._filename = strdup(filename)
+ filename = _encodeFilename(filename)
self.fastqfile = gzopen( filename, "r" )
self.entry = kseq_init( self.fastqfile )
+ self._filename = filename
def close( self ):
'''close file.'''
- if self._filename != NULL:
+ if self.entry != NULL:
gzclose( self.fastqfile )
- free(self._filename)
+ if self.entry:
+ kseq_destroy(self.entry)
+ self.entry = NULL
def __dealloc__(self):
- kseq_destroy(self.entry)
self.close()
property filename:
'''number of :term:`filename` associated with this object.'''
def __get__(self):
- if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
return self._filename
def __iter__(self):
@@ -701,7 +730,7 @@ cdef class Samfile:
def __cinit__(self, *args, **kwargs ):
self.samfile = NULL
- self._filename = NULL
+ self._filename = None
self.isbam = False
self.isstream = False
self._open( *args, **kwargs )
@@ -759,27 +788,19 @@ cdef class Samfile:
assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode
- #assert filename != NULL
-
# close a previously opened file
if self.samfile != NULL: self.close()
- self.samfile = NULL
cdef bam_header_t * header_to_write
header_to_write = NULL
- if self._filename != NULL: free(self._filename )
- filename = _my_encodeFilename(filename)
cdef bytes bmode = mode.encode('ascii')
- #cdef char* cfilename
- #cfilename = filename.encode(_FILENAME_ENCODING)
- self._filename = strdup(filename)
- self.isstream = strcmp( filename, "-" ) == 0
+ self._filename = filename = _encodeFilename(filename)
+ self.isstream = filename == b"-"
self.isbam = len(mode) > 1 and mode[1] == 'b'
- self.isremote = strncmp(filename,"http:",5) == 0 or \
- strncmp(filename,"ftp:",4) == 0
+ self.isremote = filename.startswith(b"http:") or filename.startswith(b"ftp:")
cdef char * ctext
ctext = NULL
@@ -819,7 +840,9 @@ cdef class Samfile:
if text is None and add_sq_text:
text = []
for x from 0 <= x < header_to_write.n_targets:
- text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
+ text.append( "@SQ\tSN:%s\tLN:%s\n" % \
+ (_force_str(referencenames[x]),
+ referencelengths[x] ) )
text = ''.join(text)
if text != None:
@@ -845,9 +868,7 @@ cdef class Samfile:
elif mode[0] == "r":
# open file for reading
- if strncmp( filename, "-", 1) != 0 and \
- not self.isremote and \
- not os.path.exists( filename ):
+ if filename != b"-" and not self.isremote and not os.path.exists( filename ):
raise IOError( "file `%s` not found" % filename)
# try to detect errors
@@ -1270,7 +1291,6 @@ cdef class Samfile:
# note: __del__ is not called.
self.close()
bam_destroy1(self.b)
- if self._filename != NULL: free( self._filename )
cpdef int write( self, AlignedRead read ) except -1:
'''
@@ -1298,7 +1318,6 @@ cdef class Samfile:
property filename:
'''number of :term:`filename` associated with this object.'''
def __get__(self):
- if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
return self._filename
property nreferences:
@@ -2604,9 +2623,12 @@ cdef class AlignedRead:
p[k] = <uint8_t>q[k] - 33
property query:
- """aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).
+ """aligned portion of the read and excludes any flanking bases
+ that were :term:`soft clipped` (None if not present).
- 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.
+ 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.
SAM/BAM files may included extra flanking bases sequences that were
not part of the alignment. These bases may be the result of the
@@ -2630,7 +2652,8 @@ cdef class AlignedRead:
return get_seq_range(src, start, end)
property qqual:
- """aligned query sequence quality values (None if not present). This property is read-only.
+ """aligned query sequence quality values (None if not
+ present). This property is read-only.
In Python 3, this property is of type bytes."""
def __get__(self):
diff --git a/pysam/ctabix.c b/pysam/ctabix.c
index 3d639f2..6231c76 100644
--- a/pysam/ctabix.c
+++ b/pysam/ctabix.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
+/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -260,10 +260,12 @@
#include "fcntl.h"
#include "unistd.h"
#include "stdint.h"
+#include "zlib.h"
#include "bgzf.h"
#include "tabix.h"
#include "tabix_util.h"
#include "pythread.h"
+#include "errno.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */
@@ -348,79 +350,25 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_6ctabix_Parser;
-struct __pyx_obj_5pysam_6ctabix_asBed;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
struct __pyx_obj_5pysam_6ctabix_TabixIterator;
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_5pysam_6ctabix_Parser;
+struct __pyx_obj_5pysam_6ctabix_asGTF;
struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
-struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
struct __pyx_obj_5pysam_6ctabix_Tabixfile;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
struct __pyx_obj_5pysam_10TabProxies_BedProxy;
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
-struct __pyx_obj_5pysam_6ctabix_asTuple;
-
-/* "pysam/ctabix.pxd":190
- * cdef tabix_t * tabixfile
- *
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_Parser {
- PyObject_HEAD
-};
-
-
-/* "pysam/ctabix.pxd":199
- * pass
- *
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asBed {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "pysam/ctabix.pxd":202
- * pass
- *
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asVCF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
+struct __pyx_obj_5pysam_6ctabix_asBed;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
-/* "pysam/ctabix.pxd":210
+/* "pysam/ctabix.pxd":224
* cdef Parser parser
*
- * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
- */
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
- FILE *infile;
- char *buffer;
- size_t size;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
-};
-
-
-/* "pysam/ctabix.pxd":182
- * cdef char * _filename
- *
* cdef class TabixIterator: # <<<<<<<<<<<<<<
* cdef ti_iter_t iterator
* cdef tabix_t * tabixfile
@@ -432,17 +380,28 @@ struct __pyx_obj_5pysam_6ctabix_TabixIterator {
};
-/* "pysam/ctabix.pxd":186
+/* "pysam/ctabix.pxd":232
* cdef tabix_t * tabixfile
*
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * cdef parse( self, char * buffer, int len )
+ *
*/
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
+struct __pyx_obj_5pysam_6ctabix_Parser {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtab;
+};
+
+
+/* "pysam/ctabix.pxd":239
+ *
+ *
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asGTF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
@@ -480,46 +439,40 @@ struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
};
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
- *
- * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
-};
-
-
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+/* "pysam/ctabix.pxd":201
+ * int ks_getuntil( kstream_t *, int, kstring_t *, int * )
*
- * cdef:
+ * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
+ * cdef gzFile fh
+ * cdef kstream_t * ks
*/
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtab;
+ gzFile fh;
+ kstream_t *ks;
+ kstring_t buffer;
+ size_t size;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+ int fd;
+ PyObject *infile;
};
-/* "pysam/ctabix.pxd":196
+/* "pysam/ctabix.pxd":245
* pass
*
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_asGTF {
+struct __pyx_obj_5pysam_6ctabix_asVCF {
struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "pysam/ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+/* "pysam/ctabix.pxd":212
+ * cdef __cnext__(self)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
*
@@ -530,10 +483,23 @@ struct __pyx_obj_5pysam_6ctabix_Tabixfile {
tabix_t *tabixfile;
int isremote;
char *_filename;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+};
+
+
+/* "pysam/ctabix.pxd":235
+ * cdef parse( self, char * buffer, int len )
+ *
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * cdef parse( self, char * buffer, int len )
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "pysam/ctabix.pxd":205
+/* "pysam/ctabix.pxd":248
* pass
*
* cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
@@ -548,6 +514,32 @@ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
};
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( self )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+};
+
+
+/* "pysam/ctabix.pxd":228
+ * cdef tabix_t * tabixfile
+ *
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
+ */
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
+};
+
+
/* "TabProxies.pxd":72
* pass
*
@@ -564,32 +556,101 @@ struct __pyx_obj_5pysam_10TabProxies_BedProxy {
};
-/* "pysam/ctabix.pxd":218
- * cdef __cnext__(self)
+/* "pysam/ctabix.pxd":242
+ * pass
+ *
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_6ctabix_asBed {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "pysam/ctabix.pxd":193
- * pass
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
+};
+
+
+
+/* "pysam/ctabix.pyx":392
+ * #########################################################
+ * #########################################################
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ *
+ * cdef parse(self, char * buffer, int length):
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_Parser {
+ PyObject *(*parse)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int);
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtabptr_5pysam_6ctabix_Parser;
+
+
+/* "pysam/ctabix.pyx":400
+ * return self.parse( buffer, length )
*
* cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * pass
+ * '''converts a :term:`tabix row` into a python tuple.
*
*/
-struct __pyx_obj_5pysam_6ctabix_asTuple {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+
+struct __pyx_vtabstruct_5pysam_6ctabix_asTuple {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asTuple *__pyx_vtabptr_5pysam_6ctabix_asTuple;
+
+
+/* "pysam/ctabix.pyx":450
+ * return r
+ *
+ * cdef class asBed( Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a bed record
+ * with the following fields:
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_asBed {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asBed *__pyx_vtabptr_5pysam_6ctabix_asBed;
+
+
+/* "pysam/ctabix.pyx":802
+ *
+ *
+ * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over a compressed or uncompressed ``infile``.
+ * '''
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *);
};
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator;
+
+
+/* "pysam/ctabix.pyx":490
+ * return r
+ *
+ * cdef class asVCF( Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a VCF record with
+ * the following fields:
+ */
+struct __pyx_vtabstruct_5pysam_6ctabix_asVCF {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asVCF *__pyx_vtabptr_5pysam_6ctabix_asVCF;
/* "TabProxies.pxd":41
@@ -624,34 +685,6 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-
-struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
- struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
-};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-
-
-/* "pysam/ctabix.pyx":709
- * ## Iterators for parsing through unindexed files.
- * #########################################################
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
- *
- */
-
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
-};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
-
-
/* "TabProxies.pxd":72
* pass
*
@@ -666,18 +699,18 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
-/* "pysam/ctabix.pyx":771
- * return self.__cnext__()
- *
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
+/* "pysam/ctabix.pyx":413
+ * return r
*
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a GTF record with the following
+ * fields:
*/
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *);
+struct __pyx_vtabstruct_5pysam_6ctabix_asGTF {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_asGTF *__pyx_vtabptr_5pysam_6ctabix_asGTF;
/* "TabProxies.pxd":60
@@ -693,6 +726,20 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
+
+
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -770,6 +817,8 @@ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
@@ -1100,7 +1149,12 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'cpython' */
+/* Module declarations from 'libc.errno' */
+
+/* Module declarations from 'libc.stdint' */
+
/* Module declarations from 'pysam.ctabix' */
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_file_iterator = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0;
@@ -1110,8 +1164,6 @@ static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0;
static PyObject *__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = 0;
static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *); /*proto*/
static PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *); /*proto*/
@@ -1123,13 +1175,14 @@ int __pyx_module_is_main_pysam__ctabix = 0;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_IOError;
+static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_IndexError;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_OSError;
static PyObject *__pyx_builtin_ord;
-static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_MemoryError;
-static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_parser, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
@@ -1147,23 +1200,18 @@ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_
static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
static void __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_6Parser___call__(struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length); /* proto */
static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
static void __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */
-static int __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_6ctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_6ctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_8next(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
@@ -1180,26 +1228,27 @@ static char __pyx_k_14[] = "file `%s` not found";
static char __pyx_k_15[] = "index `%s` not found";
static char __pyx_k_16[] = "could not open file `%s`";
static char __pyx_k_17[] = "%s:%i-%i";
-static char __pyx_k_18[] = "invalid region `%s`";
-static char __pyx_k_19[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_20[] = "start out of range (%i)";
-static char __pyx_k_21[] = "end out of range (%i)";
-static char __pyx_k_22[] = "I/O operation on closed file";
-static char __pyx_k_25[] = "malformatted query or wrong sequence name.\n";
-static char __pyx_k_27[] = "can't open header.\n";
-static char __pyx_k_31[] = "Filename '%s' already exists, use *force* to overwrite";
-static char __pyx_k_32[] = "could not open '%s' for writing";
-static char __pyx_k_34[] = "could not open '%s' for reading";
-static char __pyx_k_36[] = "writing failed";
-static char __pyx_k_40[] = "#";
-static char __pyx_k_42[] = "No such file '%s'";
-static char __pyx_k_43[] = "neither preset nor seq_col,start_col and end_col given";
-static char __pyx_k_45[] = ".gz";
-static char __pyx_k_47[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
-static char __pyx_k_49[] = "unknown preset '%s', valid presets are '%s'";
-static char __pyx_k_50[] = ",";
+static char __pyx_k_18[] = "invalid region: start (%i) > end (%i)";
+static char __pyx_k_19[] = "start out of range (%i)";
+static char __pyx_k_20[] = "end out of range (%i)";
+static char __pyx_k_21[] = "I/O operation on closed file";
+static char __pyx_k_24[] = "malformatted query or wrong sequence name.\n";
+static char __pyx_k_26[] = "can't open header.\n";
+static char __pyx_k_30[] = "Filename '%s' already exists, use *force* to overwrite";
+static char __pyx_k_31[] = "could not open '%s' for writing";
+static char __pyx_k_33[] = "could not open '%s' for reading";
+static char __pyx_k_35[] = "writing failed";
+static char __pyx_k_39[] = "#";
+static char __pyx_k_41[] = "No such file '%s'";
+static char __pyx_k_42[] = "neither preset nor seq_col,start_col and end_col given";
+static char __pyx_k_44[] = ".gz";
+static char __pyx_k_46[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
+static char __pyx_k_48[] = "unknown preset '%s', valid presets are '%s'";
+static char __pyx_k_49[] = ",";
+static char __pyx_k_50[] = "error (%d): %s (%d: %s)";
static char __pyx_k_51[] = "I/O operation on closed file.";
-static char __pyx_k_54[] = "incomplete line at %s";
+static char __pyx_k_54[] = "%s";
+static char __pyx_k_57[] = "incomplete line at %s";
static char __pyx_k_58[] = "tabix_generic_iterator";
static char __pyx_k_59[] = "filename associated with this object.";
static char __pyx_k_60[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
@@ -1212,7 +1261,6 @@ static char __pyx_k_74[] = "tabix_generic_iterator.__iter__";
static char __pyx_k_77[] = "tabix_generic_iterator.__next__";
static char __pyx_k_80[] = "tabix_generic_iterator.next";
static char __pyx_k_81[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
-static char __pyx_k_84[] = "tabix_inplace_iterator";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__r[] = "r";
@@ -1226,7 +1274,6 @@ static char __pyx_k__bed[] = "bed";
static char __pyx_k__cpy[] = "cpy";
static char __pyx_k__end[] = "end";
static char __pyx_k__gff[] = "gff";
-static char __pyx_k__len[] = "len";
static char __pyx_k__ord[] = "ord";
static char __pyx_k__sam[] = "sam";
static char __pyx_k__sys[] = "sys";
@@ -1249,7 +1296,6 @@ static char __pyx_k__close[] = "close";
static char __pyx_k__force[] = "force";
static char __pyx_k__start[] = "start";
static char __pyx_k__types[] = "types";
-static char __pyx_k__Parser[] = "Parser";
static char __pyx_k__buffer[] = "buffer";
static char __pyx_k__closed[] = "closed";
static char __pyx_k__ctypes[] = "ctypes";
@@ -1258,6 +1304,7 @@ static char __pyx_k__encode[] = "encode";
static char __pyx_k__exists[] = "exists";
static char __pyx_k__fd_src[] = "fd_src";
static char __pyx_k__infile[] = "infile";
+static char __pyx_k__length[] = "length";
static char __pyx_k__nbytes[] = "nbytes";
static char __pyx_k__parser[] = "parser";
static char __pyx_k__pileup[] = "pileup";
@@ -1273,7 +1320,6 @@ static char __pyx_k____all__[] = "__all__";
static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k__asTuple[] = "asTuple";
static char __pyx_k__end_col[] = "end_col";
-static char __pyx_k__present[] = "present";
static char __pyx_k__seq_col[] = "seq_col";
static char __pyx_k__KeyError[] = "KeyError";
static char __pyx_k__O_RDONLY[] = "O_RDONLY";
@@ -1295,6 +1341,7 @@ static char __pyx_k__reference[] = "reference";
static char __pyx_k__start_col[] = "start_col";
static char __pyx_k__tabixfile[] = "tabixfile";
static char __pyx_k__zerobased[] = "zerobased";
+static char __pyx_k__IndexError[] = "IndexError";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__MemoryError[] = "MemoryError";
@@ -1310,6 +1357,7 @@ static char __pyx_k__tabix_compress[] = "tabix_compress";
static char __pyx_k__tabix_iterator[] = "tabix_iterator";
static char __pyx_k__getdefaultencoding[] = "getdefaultencoding";
static char __pyx_k__NotImplementedError[] = "NotImplementedError";
+static char __pyx_k__tabix_file_iterator[] = "tabix_file_iterator";
static PyObject *__pyx_kp_u_1;
static PyObject *__pyx_kp_s_12;
static PyObject *__pyx_kp_s_14;
@@ -1320,24 +1368,25 @@ static PyObject *__pyx_kp_s_18;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_20;
static PyObject *__pyx_kp_s_21;
-static PyObject *__pyx_kp_s_22;
-static PyObject *__pyx_kp_s_25;
-static PyObject *__pyx_kp_s_27;
+static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_kp_s_26;
static PyObject *__pyx_kp_u_3;
+static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_31;
-static PyObject *__pyx_kp_s_32;
-static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_36;
-static PyObject *__pyx_kp_s_40;
+static PyObject *__pyx_kp_s_33;
+static PyObject *__pyx_kp_s_35;
+static PyObject *__pyx_kp_s_39;
+static PyObject *__pyx_kp_s_41;
static PyObject *__pyx_kp_s_42;
-static PyObject *__pyx_kp_s_43;
-static PyObject *__pyx_kp_s_45;
-static PyObject *__pyx_kp_s_47;
+static PyObject *__pyx_kp_s_44;
+static PyObject *__pyx_kp_s_46;
+static PyObject *__pyx_kp_s_48;
static PyObject *__pyx_kp_s_49;
static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_kp_s_50;
static PyObject *__pyx_kp_s_51;
static PyObject *__pyx_kp_s_54;
+static PyObject *__pyx_kp_s_57;
static PyObject *__pyx_n_s_58;
static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_n_s_62;
@@ -1349,16 +1398,15 @@ static PyObject *__pyx_n_s_74;
static PyObject *__pyx_n_s_77;
static PyObject *__pyx_n_s_80;
static PyObject *__pyx_kp_s_81;
-static PyObject *__pyx_n_s_84;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__IOError;
+static PyObject *__pyx_n_s__IndexError;
static PyObject *__pyx_n_s__KeyError;
static PyObject *__pyx_n_s__MemoryError;
static PyObject *__pyx_n_s__NotImplementedError;
static PyObject *__pyx_n_s__OSError;
static PyObject *__pyx_n_s__O_RDONLY;
static PyObject *__pyx_n_s__PYTHON3;
-static PyObject *__pyx_n_s__Parser;
static PyObject *__pyx_n_s__StopIteration;
static PyObject *__pyx_n_s__Tabixfile;
static PyObject *__pyx_n_s__TypeError;
@@ -1409,7 +1457,7 @@ static PyObject *__pyx_n_s__infile;
static PyObject *__pyx_n_s__io;
static PyObject *__pyx_n_s__itertools;
static PyObject *__pyx_n_s__join;
-static PyObject *__pyx_n_s__len;
+static PyObject *__pyx_n_s__length;
static PyObject *__pyx_n_s__line;
static PyObject *__pyx_n_s__meta_char;
static PyObject *__pyx_n_s__mode;
@@ -1420,7 +1468,6 @@ static PyObject *__pyx_n_s__os;
static PyObject *__pyx_n_s__parser;
static PyObject *__pyx_n_s__path;
static PyObject *__pyx_n_s__pileup;
-static PyObject *__pyx_n_s__present;
static PyObject *__pyx_n_s__preset;
static PyObject *__pyx_n_s__preset2conf;
static PyObject *__pyx_n_s__psltbl;
@@ -1438,6 +1485,7 @@ static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__struct;
static PyObject *__pyx_n_s__sys;
static PyObject *__pyx_n_s__tabix_compress;
+static PyObject *__pyx_n_s__tabix_file_iterator;
static PyObject *__pyx_n_s__tabix_index;
static PyObject *__pyx_n_s__tabix_iterator;
static PyObject *__pyx_n_s__tabixfile;
@@ -1459,33 +1507,33 @@ static PyObject *__pyx_int_15;
static PyObject *__pyx_int_17;
static PyObject *__pyx_int_18;
static PyObject *__pyx_int_35;
+static PyObject *__pyx_int_64;
static PyObject *__pyx_int_65536;
-static PyObject *__pyx_k_30;
-static PyObject *__pyx_k_39;
-static PyObject *__pyx_k_41;
+static PyObject *__pyx_k_29;
+static PyObject *__pyx_k_38;
+static PyObject *__pyx_k_40;
static PyObject *__pyx_k_tuple_2;
static PyObject *__pyx_k_tuple_4;
static PyObject *__pyx_k_tuple_8;
static PyObject *__pyx_k_tuple_10;
static PyObject *__pyx_k_tuple_11;
static PyObject *__pyx_k_tuple_13;
+static PyObject *__pyx_k_tuple_22;
static PyObject *__pyx_k_tuple_23;
-static PyObject *__pyx_k_tuple_24;
-static PyObject *__pyx_k_tuple_26;
+static PyObject *__pyx_k_tuple_25;
+static PyObject *__pyx_k_tuple_27;
static PyObject *__pyx_k_tuple_28;
-static PyObject *__pyx_k_tuple_29;
-static PyObject *__pyx_k_tuple_33;
-static PyObject *__pyx_k_tuple_35;
+static PyObject *__pyx_k_tuple_32;
+static PyObject *__pyx_k_tuple_34;
+static PyObject *__pyx_k_tuple_36;
static PyObject *__pyx_k_tuple_37;
-static PyObject *__pyx_k_tuple_38;
-static PyObject *__pyx_k_tuple_44;
-static PyObject *__pyx_k_tuple_46;
-static PyObject *__pyx_k_tuple_48;
+static PyObject *__pyx_k_tuple_43;
+static PyObject *__pyx_k_tuple_45;
+static PyObject *__pyx_k_tuple_47;
static PyObject *__pyx_k_tuple_52;
static PyObject *__pyx_k_tuple_53;
static PyObject *__pyx_k_tuple_55;
static PyObject *__pyx_k_tuple_56;
-static PyObject *__pyx_k_tuple_57;
static PyObject *__pyx_k_tuple_63;
static PyObject *__pyx_k_tuple_67;
static PyObject *__pyx_k_tuple_69;
@@ -1501,7 +1549,7 @@ static PyObject *__pyx_k_codeobj_76;
static PyObject *__pyx_k_codeobj_79;
static PyObject *__pyx_k_codeobj_83;
-/* "pysam/ctabix.pyx":19
+/* "pysam/ctabix.pyx":24
* from cpython.version cimport PY_MAJOR_VERSION
*
* cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<<
@@ -1519,7 +1567,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("from_string_and_size", 0);
- /* "pysam/ctabix.pyx":20
+ /* "pysam/ctabix.pyx":25
*
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -1529,7 +1577,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "pysam/ctabix.pyx":21
+ /* "pysam/ctabix.pyx":26
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3:
* return s[:length] # <<<<<<<<<<<<<<
@@ -1537,7 +1585,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
* return s[:length].decode("ascii")
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1546,7 +1594,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
}
/*else*/ {
- /* "pysam/ctabix.pyx":23
+ /* "pysam/ctabix.pyx":28
* return s[:length]
* else:
* return s[:length].decode("ascii") # <<<<<<<<<<<<<<
@@ -1554,7 +1602,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
* # filename encoding (copied from lxml.etree.pyx)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1574,7 +1622,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
return __pyx_r;
}
-/* "pysam/ctabix.pyx":36
+/* "pysam/ctabix.pyx":41
* #_C_FILENAME_ENCODING = <char*>_FILENAME_ENCODING
*
* cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<<
@@ -1594,7 +1642,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_my_encodeFilename", 0);
- /* "pysam/ctabix.pyx":39
+ /* "pysam/ctabix.pyx":44
* u"""Make sure a filename is 8-bit encoded (or None).
* """
* if filename is None: # <<<<<<<<<<<<<<
@@ -1604,7 +1652,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
__pyx_t_1 = (__pyx_v_filename == Py_None);
if (__pyx_t_1) {
- /* "pysam/ctabix.pyx":40
+ /* "pysam/ctabix.pyx":45
* """
* if filename is None:
* return None # <<<<<<<<<<<<<<
@@ -1618,7 +1666,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
goto __pyx_L3;
}
- /* "pysam/ctabix.pyx":41
+ /* "pysam/ctabix.pyx":46
* if filename is None:
* return None
* elif PyBytes_Check(filename): # <<<<<<<<<<<<<<
@@ -1628,7 +1676,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
__pyx_t_1 = PyBytes_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "pysam/ctabix.pyx":42
+ /* "pysam/ctabix.pyx":47
* return None
* elif PyBytes_Check(filename):
* return filename # <<<<<<<<<<<<<<
@@ -1636,14 +1684,14 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
* return filename.encode(_FILENAME_ENCODING)
*/
__Pyx_XDECREF(((PyObject *)__pyx_r));
- if (!(likely(PyBytes_CheckExact(__pyx_v_filename))||((__pyx_v_filename) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_filename)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_v_filename))||((__pyx_v_filename) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_v_filename)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_v_filename);
__pyx_r = ((PyObject*)__pyx_v_filename);
goto __pyx_L0;
goto __pyx_L3;
}
- /* "pysam/ctabix.pyx":43
+ /* "pysam/ctabix.pyx":48
* elif PyBytes_Check(filename):
* return filename
* elif PyUnicode_Check(filename): # <<<<<<<<<<<<<<
@@ -1653,7 +1701,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
__pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "pysam/ctabix.pyx":44
+ /* "pysam/ctabix.pyx":49
* return filename
* elif PyUnicode_Check(filename):
* return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<<
@@ -1661,18 +1709,18 @@ static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_fil
* raise TypeError, u"Argument must be string or unicode."
*/
__Pyx_XDECREF(((PyObject *)__pyx_r));
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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return __pyx_r;
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if (__pyx_t_1) {
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if (__pyx_t_1) {
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return __pyx_r;
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goto __pyx_L4;
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+ /* "pysam/ctabix.pyx":197
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+ __pyx_t_2 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_5);
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__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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goto __pyx_L8;
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- * if not 0 <= rend < max_pos: raise ValueError( 'end out of range (%i)' % rend ) # <<<<<<<<<<<<<<
+ * if not 0 <= rstart < max_pos: raise IndexError( 'start out of range (%i)' % rstart )
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}
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if (__pyx_t_1) {
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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goto __pyx_L9;
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__pyx_L9:;
@@ -3304,34 +3382,34 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_o
}
__pyx_L5:;
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+ /* "pysam/ctabix.pyx":200
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__pyx_t_2 = 0;
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@@ -3354,7 +3432,7 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_o
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static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+static char __pyx_doc_5pysam_6ctabix_9Tabixfile_8fetch[] = "Tabixfile.fetch(self, reference=None, start=None, end=None, region=None, parser=None)\n\n \n fetch one or more rows in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Without *reference* or *region* all entries will be fetched. \n \n If only *reference* [...]
static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
@@ -3368,7 +3446,7 @@ static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_sel
static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__parser,0};
PyObject* values[5] = {0,0,0,0,0};
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+ /* "pysam/ctabix.pyx":203
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* def fetch( self,
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*/
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+ /* "pysam/ctabix.pyx":204
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*/
values[1] = ((PyObject *)Py_None);
- /* "pysam/ctabix.pyx":193
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*/
values[2] = ((PyObject *)Py_None);
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values[3] = ((PyObject *)Py_None);
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switch (PyTuple_GET_SIZE(__pyx_args)) {
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+ __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
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PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
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__Pyx_GIVEREF(__pyx_v_region);
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if (size > 4) __Pyx_RaiseTooManyValuesError(4);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(item);
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Py_ssize_t index = -1;
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PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_self));
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__Pyx_GIVEREF(__pyx_v_rend);
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if (__pyx_t_4) {
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_5pysam_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L0;
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return __pyx_r;
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__Pyx_RefNannySetupContext("__cinit__", 0);
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__pyx_t_4 = __pyx_v_tabixfile->tabixfile;
__pyx_v_self->tabixfile = __pyx_t_4;
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__pyx_t_3 = (__pyx_v_tid < 0);
if (__pyx_t_3) {
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bgzf_seek(__pyx_v_self->tabixfile->fp, 0, 0);
- /* "pysam/ctabix.pyx":297
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}
/*else*/ {
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__pyx_t_3 = (((void *)__pyx_v_self->iterator) == NULL);
if (__pyx_t_3) {
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goto __pyx_L4;
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return __pyx_r;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__", 0);
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return __pyx_r;
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int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__next__", 0);
- /* "pysam/ctabix.pyx":320
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+ /* "pysam/ctabix.pyx":334
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while (1) {
if (!1) break;
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* # simply use '#' for now.
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__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
- /* "pysam/ctabix.pyx":322
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__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L5;
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__pyx_L4_break:;
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+ __pyx_t_2 = __pyx_f_5pysam_6ctabix__charptr_to_str(__pyx_v_s); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_retval = __pyx_t_2;
__pyx_t_2 = 0;
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__Pyx_RefNannyFinishContext();
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-/* "pysam/ctabix.pyx":328
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int __pyx_t_1;
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "pysam/ctabix.pyx":329
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__pyx_t_1 = (((void *)__pyx_v_self->iterator) != NULL);
if (__pyx_t_1) {
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goto __pyx_L5_argtuple_error;
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.ctabix.TabixHeaderIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
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return __pyx_r;
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__Pyx_RefNannySetupContext("__cinit__", 0);
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__pyx_t_4 = __pyx_v_tabixfile->tabixfile;
__pyx_v_self->tabixfile = __pyx_t_4;
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__pyx_v_self->iterator = ti_query(__pyx_v_self->tabixfile, NULL, 0, 0);
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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*/
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__pyx_t_6 = (__pyx_v_c > 0);
if (!__pyx_t_6) break;
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*/
__pyx_v_c = read(__pyx_v_fd_src, __pyx_v_buffer, __pyx_v_WINDOW_SIZE);
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+ /* "pysam/ctabix.pyx":620
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+ /* "pysam/ctabix.pyx":621
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*/
free(__pyx_v_buffer);
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PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.tabix_file_iterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_tabix_file_iterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9398,24 +8973,24 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TabixIterator, /*tp_as_number*/
- &__pyx_tp_as_sequence_TabixIterator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TabixIterator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_tabix_file_iterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_tabix_file_iterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_tabix_file_iterator, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TabixIterator, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("iterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_tabix_file_iterator, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterate over a compressed or uncompressed ``infile``.\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_6ctabix_tabix_file_iterator, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_6ctabix_tabix_file_iterator, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_TabixIterator, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_19tabix_file_iterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_19tabix_file_iterator_7__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_tabix_file_iterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9425,7 +9000,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_tabix_file_iterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9439,34 +9014,82 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_Tabixfile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- if (__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o);
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_Tabixfile *p = (struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(o);
+ __pyx_pw_5pysam_6ctabix_9Tabixfile_13__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixHeaderIterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__)},
+static int __pyx_tp_traverse_5pysam_6ctabix_Tabixfile(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_6ctabix_Tabixfile *p = (struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o;
+ if (p->parser) {
+ e = (*v)(((PyObject*)p->parser), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_6ctabix_Tabixfile(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_Tabixfile *p = (struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->parser);
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_6ctabix_9Tabixfile_8filename_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_5pysam_6ctabix_Tabixfile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_2_isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_4_open)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_7_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_6_parseRegion)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_8fetch)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_11close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_10close)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = {
+static struct PyGetSetDef __pyx_getsets_5pysam_6ctabix_Tabixfile[] = {
+ {(char *)"filename", __pyx_getprop_5pysam_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_59), 0},
+ {(char *)"header", __pyx_getprop_5pysam_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_60), 0},
+ {(char *)"contigs", __pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_61), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Tabixfile = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -9524,7 +9147,7 @@ static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = {
+static PySequenceMethods __pyx_tp_as_sequence_Tabixfile = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -9537,13 +9160,13 @@ static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_TabixHeaderIterator = {
+static PyMappingMethods __pyx_tp_as_mapping_Tabixfile = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
+static PyBufferProcs __pyx_tp_as_buffer_Tabixfile = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -9564,12 +9187,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_Tabixfile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.TabixHeaderIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.Tabixfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9579,26 +9202,26 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TabixHeaderIterator, /*tp_as_number*/
- &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TabixHeaderIterator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Tabixfile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Tabixfile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Tabixfile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_Tabixfile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename, mode='r', parser = None)*\n\n opens a :term:`tabix file` for reading. A missing\n index (*filename* + \".tbi\") will raise an exception.\n\n *parser* sets the default parser for this tabix file. If *parser*\n is None, the results are returned as an unparsed string.\n Otherwise, *parser* is assumed to be a functor that will return\n parsed data (see for example :meth:`asTuple` and :meth:`asGTF`).\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_6ctabix_Tabixfile, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_6ctabix_Tabixfile, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_TabixHeaderIterator, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_Tabixfile, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_5pysam_6ctabix_Tabixfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -9606,7 +9229,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_Tabixfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9620,21 +9243,34 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ if (__pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
return o;
}
-static void __pyx_tp_dealloc_5pysam_6ctabix_Parser(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_5pysam_6ctabix_13TabixIterator_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_Parser[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_Parser = {
+static PyNumberMethods __pyx_tp_as_number_TabixIterator = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -9692,7 +9328,7 @@ static PyNumberMethods __pyx_tp_as_number_Parser = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Parser = {
+static PySequenceMethods __pyx_tp_as_sequence_TabixIterator = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -9705,13 +9341,13 @@ static PySequenceMethods __pyx_tp_as_sequence_Parser = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_Parser = {
+static PyMappingMethods __pyx_tp_as_mapping_TabixIterator = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Parser = {
+static PyBufferProcs __pyx_tp_as_buffer_TabixIterator = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -9732,12 +9368,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Parser = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.Parser"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9747,24 +9383,24 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_Parser, /*tp_as_number*/
- &__pyx_tp_as_sequence_Parser, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Parser, /*tp_as_mapping*/
+ &__pyx_tp_as_number_TabixIterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixIterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TabixIterator, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Parser, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_TabixIterator, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- 0, /*tp_doc*/
+ __Pyx_DOCSTR("iterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_Parser, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_TabixIterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9774,7 +9410,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_Parser, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9788,17 +9424,34 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ if (__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
return o;
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_asTuple[] = {
+static void __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixHeaderIterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asTuple = {
+static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -9856,7 +9509,7 @@ static PyNumberMethods __pyx_tp_as_number_asTuple = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
+static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -9869,13 +9522,13 @@ static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asTuple = {
+static PyMappingMethods __pyx_tp_as_mapping_TabixHeaderIterator = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
+static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -9896,12 +9549,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.asTuple"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.TabixHeaderIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9911,24 +9564,24 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asTuple, /*tp_as_number*/
- &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
+ &__pyx_tp_as_number_TabixHeaderIterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TabixHeaderIterator, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_5pysam_6ctabix_7asTuple_1__call__, /*tp_call*/
+ 0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_asTuple, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_TabixHeaderIterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9938,7 +9591,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_asTuple, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9951,18 +9604,26 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_vtable_5pysam_6ctabix_Parser;
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_Parser *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_6ctabix_Parser *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_Parser;
return o;
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_asGTF[] = {
+static void __pyx_tp_dealloc_5pysam_6ctabix_Parser(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static PyMethodDef __pyx_methods_5pysam_6ctabix_Parser[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asGTF = {
+static PyNumberMethods __pyx_tp_as_number_Parser = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -10020,7 +9681,7 @@ static PyNumberMethods __pyx_tp_as_number_asGTF = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
+static PySequenceMethods __pyx_tp_as_sequence_Parser = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -10033,13 +9694,13 @@ static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asGTF = {
+static PyMappingMethods __pyx_tp_as_mapping_Parser = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
+static PyBufferProcs __pyx_tp_as_buffer_Parser = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -10060,10 +9721,10 @@ static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.asGTF"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.Parser"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
@@ -10075,24 +9736,24 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asGTF, /*tp_as_number*/
- &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Parser, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Parser, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Parser, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_5pysam_6ctabix_5asGTF_1__call__, /*tp_call*/
+ __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_Parser, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record with the following \n fields:\n\n contig\n contig\n feature\n feature\n source\n source\n start\n genomic start coordinate (0-based)\n end\n genomic end coordinate plus one (0-based)\n score\n feature score\n strand\n strand\n frame\n frame\n attributes\n attribute string.\n\n GTF formatted entries also defined the attributes:\n\n gene_i [...]
+ 0, /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_asGTF, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_Parser, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10102,7 +9763,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_asGTF, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_Parser, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10115,18 +9776,22 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asTuple __pyx_vtable_5pysam_6ctabix_asTuple;
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_asTuple *p;
PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_6ctabix_asTuple *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asTuple;
return o;
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_asBed[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asTuple[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asBed = {
+static PyNumberMethods __pyx_tp_as_number_asTuple = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -10184,7 +9849,7 @@ static PyNumberMethods __pyx_tp_as_number_asBed = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asBed = {
+static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -10197,13 +9862,13 @@ static PySequenceMethods __pyx_tp_as_sequence_asBed = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asBed = {
+static PyMappingMethods __pyx_tp_as_mapping_asTuple = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asBed = {
+static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -10224,10 +9889,10 @@ static PyBufferProcs __pyx_tp_as_buffer_asBed = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.asBed"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asTuple"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
@@ -10239,24 +9904,28 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asBed, /*tp_as_number*/
- &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asTuple, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_5pysam_6ctabix_5asBed_1__call__, /*tp_call*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/
+ #else
+ 0, /*tp_call*/
+ #endif
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n contig\n contig\n start\n genomic start coordinate (zero-based)\n end\n genomic end coordinate plus one (zero-based)\n name\n name of feature.\n score\n score of feature\n strand\n strand of feature\n thickStart\n thickStart\n thickEnd\n thickEnd\n itemRGB\n itemRGB\n blockCount\n number of bocks\n [...]
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_asBed, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_asTuple, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10266,7 +9935,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_asBed, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asTuple, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10279,18 +9948,22 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asGTF __pyx_vtable_5pysam_6ctabix_asGTF;
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_asGTF *p;
PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_6ctabix_asGTF *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asGTF;
return o;
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_asVCF[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asGTF[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asVCF = {
+static PyNumberMethods __pyx_tp_as_number_asGTF = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -10348,7 +10021,7 @@ static PyNumberMethods __pyx_tp_as_number_asVCF = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asVCF = {
+static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -10361,13 +10034,13 @@ static PySequenceMethods __pyx_tp_as_sequence_asVCF = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asVCF = {
+static PyMappingMethods __pyx_tp_as_mapping_asGTF = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
+static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -10388,10 +10061,10 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.asVCF"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asGTF"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
@@ -10403,24 +10076,28 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asVCF, /*tp_as_number*/
- &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asGTF, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_5pysam_6ctabix_5asVCF_1__call__, /*tp_call*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/
+ #else
+ 0, /*tp_call*/
+ #endif
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n contig\n contig\n pos\n chromosomal position, zero-based\n id \n id\n ref\n reference\n alt\n alt\n qual\n qual\n filter\n filter\n info\n info\n format\n format specifier.\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample [...]
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record with the following \n fields:\n\n contig\n contig\n feature\n feature\n source\n source\n start\n genomic start coordinate (0-based)\n end\n genomic end coordinate plus one (0-based)\n score\n feature score\n strand\n strand\n frame\n frame\n attributes\n attribute string.\n\n GTF formatted entries also defined the attributes:\n\n gene_i [...]
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_asVCF, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_asGTF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10430,7 +10107,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_asVCF, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asGTF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10443,60 +10120,22 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asBed __pyx_vtable_5pysam_6ctabix_asBed;
-static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_asBed *p;
+ PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o);
- p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
+ p = ((struct __pyx_obj_5pysam_6ctabix_asBed *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asBed;
return o;
}
-static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
- PyObject_GC_UnTrack(o);
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_CLEAR(p->parser);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
- if (p->parser) {
- e = (*v)(((PyObject*)p->parser), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->parser);
- p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIteratorParsed[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asBed[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_TabixIteratorParsed = {
+static PyNumberMethods __pyx_tp_as_number_asBed = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -10554,7 +10193,7 @@ static PyNumberMethods __pyx_tp_as_number_TabixIteratorParsed = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_TabixIteratorParsed = {
+static PySequenceMethods __pyx_tp_as_sequence_asBed = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -10567,13 +10206,13 @@ static PySequenceMethods __pyx_tp_as_sequence_TabixIteratorParsed = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_TabixIteratorParsed = {
+static PyMappingMethods __pyx_tp_as_mapping_asBed = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = {
+static PyBufferProcs __pyx_tp_as_buffer_asBed = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -10594,12 +10233,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.TabixIteratorParsed"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asBed"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10609,24 +10248,28 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TabixIteratorParsed, /*tp_as_number*/
- &__pyx_tp_as_sequence_TabixIteratorParsed, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TabixIteratorParsed, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asBed, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/
0, /*tp_hash*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/
+ #else
0, /*tp_call*/
+ #endif
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TabixIteratorParsed, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed, /*tp_clear*/
+ &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n contig\n contig\n start\n genomic start coordinate (zero-based)\n end\n genomic end coordinate plus one (zero-based)\n name\n name of feature.\n score\n score of feature\n strand\n strand of feature\n thickStart\n thickStart\n thickEnd\n thickEnd\n itemRGB\n itemRGB\n blockCount\n number of bocks\n [...]
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_TabixIteratorParsed, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_asBed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10636,7 +10279,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asBed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10649,62 +10292,22 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator __pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_asVCF __pyx_vtable_5pysam_6ctabix_asVCF;
-static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_asVCF *p;
+ PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
- p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
+ p = ((struct __pyx_obj_5pysam_6ctabix_asVCF *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asVCF;
return o;
}
-static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
- PyObject_GC_UnTrack(o);
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_5__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_CLEAR(p->parser);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
- if (p->parser) {
- e = (*v)(((PyObject*)p->parser), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->parser);
- p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asVCF[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_tabix_inplace_iterator = {
+static PyNumberMethods __pyx_tp_as_number_asVCF = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -10762,7 +10365,7 @@ static PyNumberMethods __pyx_tp_as_number_tabix_inplace_iterator = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_tabix_inplace_iterator = {
+static PySequenceMethods __pyx_tp_as_sequence_asVCF = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -10775,13 +10378,13 @@ static PySequenceMethods __pyx_tp_as_sequence_tabix_inplace_iterator = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_tabix_inplace_iterator = {
+static PyMappingMethods __pyx_tp_as_mapping_asVCF = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_tabix_inplace_iterator = {
+static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -10802,12 +10405,12 @@ static PyBufferProcs __pyx_tp_as_buffer_tabix_inplace_iterator = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_inplace_iterator = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.tabix_inplace_iterator"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asVCF"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10817,24 +10420,28 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_inplace_iterator = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_tabix_inplace_iterator, /*tp_as_number*/
- &__pyx_tp_as_sequence_tabix_inplace_iterator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_tabix_inplace_iterator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asVCF, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/
0, /*tp_hash*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/
+ #else
0, /*tp_call*/
+ #endif
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_tabix_inplace_iterator, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not safe. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator, /*tp_clear*/
+ &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record with\n the following fields:\n \n contig\n contig\n pos\n chromosomal position, zero-based\n id \n id\n ref\n reference\n alt\n alt\n qual\n qual\n filter\n filter\n info\n info\n format\n format specifier.\n\n Access to genotypes is via index::\n\n contig = vcf.contig\n first_sample_genotype = vcf[0]\n second_sample [...]
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_asVCF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10844,7 +10451,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_inplace_iterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asVCF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10857,40 +10464,47 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_inplace_iterator = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator __pyx_vtable_5pysam_6ctabix_tabix_copy_iterator;
-static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p;
+static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
+ p = ((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o);
p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
+static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
PyObject_GC_UnTrack(o);
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
Py_CLEAR(p->parser);
PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
if (p->parser) {
e = (*v)(((PyObject*)p->parser), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
+static int __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
PyObject* tmp;
tmp = ((PyObject*)p->parser);
p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
@@ -10898,12 +10512,12 @@ static int __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_copy_iterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIteratorParsed[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_tabix_copy_iterator = {
+static PyNumberMethods __pyx_tp_as_number_TabixIteratorParsed = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -10961,7 +10575,7 @@ static PyNumberMethods __pyx_tp_as_number_tabix_copy_iterator = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_tabix_copy_iterator = {
+static PySequenceMethods __pyx_tp_as_sequence_TabixIteratorParsed = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -10974,13 +10588,13 @@ static PySequenceMethods __pyx_tp_as_sequence_tabix_copy_iterator = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_tabix_copy_iterator = {
+static PyMappingMethods __pyx_tp_as_mapping_TabixIteratorParsed = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_tabix_copy_iterator = {
+static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -11001,12 +10615,12 @@ static PyBufferProcs __pyx_tp_as_buffer_tabix_copy_iterator = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_copy_iterator = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.tabix_copy_iterator"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.TabixIteratorParsed"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -11016,24 +10630,24 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_copy_iterator = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_tabix_copy_iterator, /*tp_as_number*/
- &__pyx_tp_as_sequence_tabix_copy_iterator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_tabix_copy_iterator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_TabixIteratorParsed, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixIteratorParsed, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TabixIteratorParsed, /*tp_as_mapping*/
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0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_tabix_copy_iterator, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_TabixIteratorParsed, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
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- __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator, /*tp_clear*/
+ __Pyx_DOCSTR("iterates over mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_tabix_copy_iterator, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_TabixIteratorParsed, /*tp_methods*/
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0, /*tp_getset*/
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0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
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{&__pyx_kp_s_21, __pyx_k_21, sizeof(__pyx_k_21), 0, 0, 1, 0},
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- {&__pyx_kp_s_27, __pyx_k_27, sizeof(__pyx_k_27), 0, 0, 1, 0},
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{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
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{&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
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- {&__pyx_kp_s_40, __pyx_k_40, sizeof(__pyx_k_40), 0, 0, 1, 0},
+ {&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0},
+ {&__pyx_kp_s_35, __pyx_k_35, sizeof(__pyx_k_35), 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_42, __pyx_k_42, sizeof(__pyx_k_42), 0, 0, 1, 0},
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- {&__pyx_kp_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 0},
+ {&__pyx_kp_s_44, __pyx_k_44, sizeof(__pyx_k_44), 0, 0, 1, 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_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 0},
+ {&__pyx_kp_s_57, __pyx_k_57, sizeof(__pyx_k_57), 0, 0, 1, 0},
{&__pyx_n_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 1},
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
{&__pyx_n_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 1},
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{&__pyx_n_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 1},
{&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0},
- {&__pyx_n_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 1},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
+ {&__pyx_n_s__IndexError, __pyx_k__IndexError, sizeof(__pyx_k__IndexError), 0, 0, 1, 1},
{&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
{&__pyx_n_s__MemoryError, __pyx_k__MemoryError, sizeof(__pyx_k__MemoryError), 0, 0, 1, 1},
{&__pyx_n_s__NotImplementedError, __pyx_k__NotImplementedError, sizeof(__pyx_k__NotImplementedError), 0, 0, 1, 1},
{&__pyx_n_s__OSError, __pyx_k__OSError, sizeof(__pyx_k__OSError), 0, 0, 1, 1},
{&__pyx_n_s__O_RDONLY, __pyx_k__O_RDONLY, sizeof(__pyx_k__O_RDONLY), 0, 0, 1, 1},
{&__pyx_n_s__PYTHON3, __pyx_k__PYTHON3, sizeof(__pyx_k__PYTHON3), 0, 0, 1, 1},
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{&__pyx_n_s__StopIteration, __pyx_k__StopIteration, sizeof(__pyx_k__StopIteration), 0, 0, 1, 1},
{&__pyx_n_s__Tabixfile, __pyx_k__Tabixfile, sizeof(__pyx_k__Tabixfile), 0, 0, 1, 1},
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{&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1},
- {&__pyx_n_s__len, __pyx_k__len, sizeof(__pyx_k__len), 0, 0, 1, 1},
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{&__pyx_n_s__line, __pyx_k__line, sizeof(__pyx_k__line), 0, 0, 1, 1},
{&__pyx_n_s__meta_char, __pyx_k__meta_char, sizeof(__pyx_k__meta_char), 0, 0, 1, 1},
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{&__pyx_n_s__pileup, __pyx_k__pileup, sizeof(__pyx_k__pileup), 0, 0, 1, 1},
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{&__pyx_n_s__tabix_compress, __pyx_k__tabix_compress, sizeof(__pyx_k__tabix_compress), 0, 0, 1, 1},
+ {&__pyx_n_s__tabix_file_iterator, __pyx_k__tabix_file_iterator, sizeof(__pyx_k__tabix_file_iterator), 0, 0, 1, 1},
{&__pyx_n_s__tabix_index, __pyx_k__tabix_index, sizeof(__pyx_k__tabix_index), 0, 0, 1, 1},
{&__pyx_n_s__tabix_iterator, __pyx_k__tabix_iterator, sizeof(__pyx_k__tabix_iterator), 0, 0, 1, 1},
{&__pyx_n_s__tabixfile, __pyx_k__tabixfile, sizeof(__pyx_k__tabixfile), 0, 0, 1, 1},
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- __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __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 = 132; __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 = 183; __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 = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
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__Pyx_GOTREF(__pyx_k_tuple_13);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
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- /* "pysam/ctabix.pyx":836
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* def __init__(self, infile, parser ): # <<<<<<<<<<<<<<
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* self.infile = infile
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+ __pyx_k_tuple_69 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__infile), ((PyObject *)__pyx_n_s__parser)); if (unlikely(!__pyx_k_tuple_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_69);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_69));
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- /* "pysam/ctabix.pyx":842
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
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- /* "pysam/ctabix.pyx":846
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__Pyx_GOTREF(__pyx_k_tuple_75);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
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- /* "pysam/ctabix.pyx":880
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* # python version - required for python 2.7
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__Pyx_GOTREF(__pyx_k_tuple_78);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
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+ __pyx_k_codeobj_79 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__next, 931, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/ctabix.pyx":883
+ /* "pysam/ctabix.pyx":934
* return self.__next__()
*
* def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<<
* """return an iterator over all entries in a file."""
- * return tabix_generic_iterator( infile, parser )
+ * if PYTHON3:
*/
- __pyx_k_tuple_82 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__infile), ((PyObject *)__pyx_n_s__parser)); if (unlikely(!__pyx_k_tuple_82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_82 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__infile), ((PyObject *)__pyx_n_s__parser)); if (unlikely(!__pyx_k_tuple_82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_82));
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+ __pyx_k_codeobj_83 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_iterator, 934, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -11587,6 +11191,7 @@ static int __Pyx_InitGlobals(void) {
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__pyx_int_18 = PyInt_FromLong(18); if (unlikely(!__pyx_int_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__pyx_int_35 = PyInt_FromLong(35); if (unlikely(!__pyx_int_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_64 = PyInt_FromLong(64); if (unlikely(!__pyx_int_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__pyx_int_65536 = PyInt_FromLong(65536); if (unlikely(!__pyx_int_65536)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
return 0;
__pyx_L1_error:;
@@ -11668,13 +11273,19 @@ PyMODINIT_FUNC PyInit_ctabix(void)
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_file_iterator;
+ __pyx_vtable_5pysam_6ctabix_tabix_file_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *))__pyx_f_5pysam_6ctabix_19tabix_file_iterator___cnext__;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_file_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_file_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_file_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_file_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_tabix_file_iterator = &__pyx_type_5pysam_6ctabix_tabix_file_iterator;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_Tabixfile = &__pyx_type_5pysam_6ctabix_Tabixfile;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__.doc = __pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__;
@@ -11682,12 +11293,12 @@ PyMODINIT_FUNC PyInit_ctabix(void)
}
}
#endif
- if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixIterator = &__pyx_type_5pysam_6ctabix_TabixIterator;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__.doc = __pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__;
@@ -11695,31 +11306,50 @@ PyMODINIT_FUNC PyInit_ctabix(void)
}
}
#endif
- if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = &__pyx_type_5pysam_6ctabix_TabixHeaderIterator;
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- if (__Pyx_SetAttrString(__pyx_m, "Parser", (PyObject *)&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_Parser = &__pyx_vtable_5pysam_6ctabix_Parser;
+ __pyx_vtable_5pysam_6ctabix_Parser.parse = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int))__pyx_f_5pysam_6ctabix_6Parser_parse;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_Parser.tp_dict, __pyx_vtabptr_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Parser", (PyObject *)&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_Parser = &__pyx_type_5pysam_6ctabix_Parser;
+ __pyx_vtabptr_5pysam_6ctabix_asTuple = &__pyx_vtable_5pysam_6ctabix_asTuple;
+ __pyx_vtable_5pysam_6ctabix_asTuple.__pyx_base = *__pyx_vtabptr_5pysam_6ctabix_Parser;
+ __pyx_vtable_5pysam_6ctabix_asTuple.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int))__pyx_f_5pysam_6ctabix_7asTuple_parse;
__pyx_type_5pysam_6ctabix_asTuple.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asTuple", (PyObject *)&__pyx_type_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_asTuple.tp_dict, __pyx_vtabptr_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asTuple", (PyObject *)&__pyx_type_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_asTuple = &__pyx_type_5pysam_6ctabix_asTuple;
+ __pyx_vtabptr_5pysam_6ctabix_asGTF = &__pyx_vtable_5pysam_6ctabix_asGTF;
+ __pyx_vtable_5pysam_6ctabix_asGTF.__pyx_base = *__pyx_vtabptr_5pysam_6ctabix_Parser;
+ __pyx_vtable_5pysam_6ctabix_asGTF.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int))__pyx_f_5pysam_6ctabix_5asGTF_parse;
__pyx_type_5pysam_6ctabix_asGTF.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_asGTF.tp_dict, __pyx_vtabptr_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_asGTF = &__pyx_type_5pysam_6ctabix_asGTF;
+ __pyx_vtabptr_5pysam_6ctabix_asBed = &__pyx_vtable_5pysam_6ctabix_asBed;
+ __pyx_vtable_5pysam_6ctabix_asBed.__pyx_base = *__pyx_vtabptr_5pysam_6ctabix_Parser;
+ __pyx_vtable_5pysam_6ctabix_asBed.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int))__pyx_f_5pysam_6ctabix_5asBed_parse;
__pyx_type_5pysam_6ctabix_asBed.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_asBed.tp_dict, __pyx_vtabptr_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_asBed = &__pyx_type_5pysam_6ctabix_asBed;
+ __pyx_vtabptr_5pysam_6ctabix_asVCF = &__pyx_vtable_5pysam_6ctabix_asVCF;
+ __pyx_vtable_5pysam_6ctabix_asVCF.__pyx_base = *__pyx_vtabptr_5pysam_6ctabix_Parser;
+ __pyx_vtable_5pysam_6ctabix_asVCF.__pyx_base.parse = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int))__pyx_f_5pysam_6ctabix_5asVCF_parse;
__pyx_type_5pysam_6ctabix_asVCF.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_asVCF.tp_dict, __pyx_vtabptr_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_asVCF = &__pyx_type_5pysam_6ctabix_asVCF;
- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__.doc = __pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
@@ -11727,20 +11357,8 @@ PyMODINIT_FUNC PyInit_ctabix(void)
}
}
#endif
- if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = &__pyx_type_5pysam_6ctabix_TabixIteratorParsed;
- __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator;
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- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_type_5pysam_6ctabix_tabix_inplace_iterator;
- __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_copy_iterator;
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- if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = &__pyx_type_5pysam_6ctabix_tabix_copy_iterator;
/*--- Type import code ---*/
__pyx_ptype_5pysam_10TabProxies_TupleProxy = __Pyx_ImportType("pysam.TabProxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_5pysam_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11817,41 +11435,41 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__io, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/ctabix.pyx":14
- * PyObject_AsFileDescriptor
+ /* "pysam/ctabix.pyx":19
+ * from libc.stdint cimport int64_t
*
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* # from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
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- __pyx_t_1 = __Pyx_PyBool_FromLong((PY_MAJOR_VERSION >= 3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((PY_MAJOR_VERSION >= 3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PYTHON3, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/ctabix.pyx":27
+ /* "pysam/ctabix.pyx":32
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* cdef str _FILENAME_ENCODING
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- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
__Pyx_DECREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
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+ /* "pysam/ctabix.pyx":33
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding()
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@@ -11861,22 +11479,22 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__pyx_t_3 = (__pyx_v_5pysam_6ctabix__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "pysam/ctabix.pyx":29
+ /* "pysam/ctabix.pyx":34
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+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
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+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__getdefaultencoding); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
__Pyx_DECREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
@@ -11886,7 +11504,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
}
__pyx_L2:;
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if (__pyx_t_3) {
- /* "pysam/ctabix.pyx":31
+ /* "pysam/ctabix.pyx":36
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@@ -11912,161 +11530,161 @@ PyMODINIT_FUNC PyInit_ctabix(void)
}
__pyx_L3:;
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+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_index, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* '''iterate over ``infile``.
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*/
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* # python version - required for python 2.7
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* return self.__cnext__()
*
* class tabix_generic_iterator: # <<<<<<<<<<<<<<
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*
*/
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+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s_58, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/ctabix.pyx":883
+ /* "pysam/ctabix.pyx":934
* return self.__next__()
*
* def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<<
* """return an iterator over all entries in a file."""
- * return tabix_generic_iterator( infile, parser )
+ * if PYTHON3:
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_5tabix_iterator, NULL, __pyx_n_s_66); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_5tabix_iterator, NULL, __pyx_n_s_66); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/ctabix.pyx":899
+ /* "pysam/ctabix.pyx":954
* # return tabix_generic_iterator( infile, parser )
*
* __all__ = ["tabix_index", # <<<<<<<<<<<<<<
* "tabix_compress",
* "Tabixfile",
*/
- __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_index));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tabix_index));
@@ -12092,10 +11710,13 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_iterator));
PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__tabix_iterator));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__tabix_iterator));
- __Pyx_INCREF(((PyObject *)__pyx_n_s_84));
- PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_84));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s_84));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(((PyObject *)__pyx_n_s_58));
+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_58));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s_58));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_file_iterator));
+ PyList_SET_ITEM(__pyx_t_1, 9, ((PyObject *)__pyx_n_s__tabix_file_iterator));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__tabix_file_iterator));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
/* "pysam/ctabix.pyx":1
@@ -12504,6 +12125,18 @@ static void __Pyx_RaiseArgtupleInvalid(
(num_expected == 1) ? "" : "s", num_found);
}
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
+ if (unlikely(!type)) {
+ PyErr_Format(PyExc_SystemError, "Missing type object");
+ return 0;
+ }
+ if (likely(PyObject_TypeCheck(obj, type)))
+ return 1;
+ PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
+ Py_TYPE(obj)->tp_name, type->tp_name);
+ return 0;
+}
+
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
"too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
diff --git a/pysam/ctabix.pxd b/pysam/ctabix.pxd
index c10dc43..1631f43 100644
--- a/pysam/ctabix.pxd
+++ b/pysam/ctabix.pxd
@@ -74,6 +74,19 @@ cdef extern from "stdint.h":
ctypedef int uint8_t
ctypedef int uint64_t
+cdef extern from "zlib.h":
+ ctypedef void * gzFile
+ ctypedef int64_t z_off_t
+
+ int gzclose(gzFile fp)
+ int gzread(gzFile fp, void *buf, unsigned int n)
+ char *gzerror(gzFile fp, int *errnum)
+
+ gzFile gzopen( char *path, char *mode)
+ gzFile gzdopen (int fd, char *mode)
+ char * gzgets(gzFile file, char *buf, int len)
+ int gzeof( gzFile file )
+
cdef extern from "Python.h":
ctypedef struct FILE
char *fgets(char *str, int size, FILE *ifile)
@@ -169,6 +182,33 @@ cdef extern from "tabix.h":
# /* Get the data line pointed by the iterator and iterate to the next record. */
# char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+cdef extern from "tabix_util.h":
+
+ ctypedef struct kstring_t:
+ size_t l
+ size_t m
+ char * s
+
+ ctypedef struct kstream_t:
+ pass
+
+ kstream_t * ks_init( gzFile )
+
+ int ks_read( kstream_t * )
+ void ks_destroy( kstream_t * )
+ int ks_getuntil( kstream_t *, int, kstring_t *, int * )
+
+cdef class tabix_file_iterator:
+ cdef gzFile fh
+ cdef kstream_t * ks
+ cdef kstring_t buffer
+ cdef size_t size
+ cdef Parser parser
+ cdef int fd
+ cdef infile
+
+ cdef __cnext__(self)
+
cdef class Tabixfile:
# pointer to tabixfile
@@ -179,6 +219,8 @@ cdef class Tabixfile:
cdef char * _filename
+ cdef Parser parser
+
cdef class TabixIterator:
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
@@ -188,10 +230,11 @@ cdef class TabixHeaderIterator:
cdef tabix_t * tabixfile
cdef class Parser:
- pass
+ cdef parse( self, char * buffer, int len )
cdef class asTuple(Parser):
- pass
+ cdef parse( self, char * buffer, int len )
+
cdef class asGTF(Parser):
pass
@@ -206,19 +249,3 @@ cdef class TabixIteratorParsed:
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
cdef Parser parser
-
-cdef class tabix_inplace_iterator:
- cdef FILE * infile
- cdef char * buffer
- cdef size_t size
- cdef Parser parser
-
- cdef __cnext__(self)
-
-cdef class tabix_copy_iterator:
- cdef FILE * infile
- cdef Parser parser
- cdef __cnext__(self)
-
-cdef extern from "tabix_util.h":
- pass
diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx
index 6a19541..c9cf419 100644
--- a/pysam/ctabix.pyx
+++ b/pysam/ctabix.pyx
@@ -11,6 +11,11 @@ from cpython cimport PyErr_SetString, PyBytes_Check, \
PyUnicode_Check, PyBytes_FromStringAndSize, \
PyObject_AsFileDescriptor
+from libc.stdio cimport printf, fprintf, stderr
+from libc.string cimport strerror
+from libc.errno cimport errno
+from libc.stdint cimport int64_t
+
PYTHON3 = PY_MAJOR_VERSION >= 3
# from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
@@ -82,13 +87,20 @@ cdef _force_str(object s):
cdef class Tabixfile:
- '''*(filename, mode='r')*
+ '''*(filename, mode='r', parser = None)*
opens a :term:`tabix file` for reading. A missing
index (*filename* + ".tbi") will raise an exception.
+
+ *parser* sets the default parser for this tabix file. If *parser*
+ is None, the results are returned as an unparsed string.
+ Otherwise, *parser* is assumed to be a functor that will return
+ parsed data (see for example :meth:`asTuple` and :meth:`asGTF`).
'''
- def __cinit__(self, filename, mode = 'r', *args, **kwargs ):
+ def __cinit__(self, filename, mode = 'r',
+ parser = None, *args, **kwargs ):
self.tabixfile = NULL
+ self.parser = parser
self._open( filename, mode, *args, **kwargs )
def _isOpen( self ):
@@ -180,10 +192,10 @@ cdef class Tabixfile:
region = _force_bytes(region)
ti_parse_region( self.tabixfile.idx, region,
&rtid, &rstart, &rend)
- if rtid < 0: raise ValueError( "invalid region `%s`" % region )
+ if rtid < 0: raise KeyError( reference )
if rstart > rend: raise ValueError( 'invalid region: start (%i) > end (%i)' % (rstart, rend) )
- if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
- if not 0 <= rend < max_pos: raise ValueError( 'end out of range (%i)' % rend )
+ if not 0 <= rstart < max_pos: raise IndexError( 'start out of range (%i)' % rstart )
+ if not 0 <= rend < max_pos: raise IndexError( 'end out of range (%i)' % rend )
return region, rtid, rstart, rend
@@ -202,25 +214,28 @@ cdef class Tabixfile:
If only *reference* is set, all reads matching on *reference* will be fetched.
- If *parser* is None, the results are returned as an unparsed string.
- Otherwise, *parser* is assumed to be a functor that will return parsed
- data (see for example :meth:`asTuple` and :meth:`asGTF`).
+ If *parser* is None, the default parser will be used for parsing.
'''
ti_lazy_index_load( self.tabixfile )
if not self._isOpen():
raise ValueError( "I/O operation on closed file" )
+ # the following will raise errors for invalid regions
region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
- if parser == None:
+ # use default parser if no parser is specified
+ if parser == None: parser = self.parser
+
+ if parser == None:
if region:
return TabixIterator( self, rtid, rstart, rend )
else:
return TabixIterator( self, -1, 0, 0 )
else:
if region:
- return TabixIteratorParsed( self, rtid, rstart, rend, parser )
+ return TabixIteratorParsed( self, rtid, rstart,
+ rend, parser )
else:
return TabixIteratorParsed( self, -1, 0, 0, parser )
@@ -315,7 +330,6 @@ cdef class TabixIterator:
# metachar filtering does not work within tabix
# though it should. Getting the metachar is a pain
# as ti_index_t is incomplete type.
-
# simply use '#' for now.
while 1:
s = ti_read(self.tabixfile, self.iterator, &len)
@@ -376,14 +390,19 @@ cdef class TabixHeaderIterator:
#########################################################
#########################################################
cdef class Parser:
- pass
+
+ cdef parse(self, char * buffer, int length):
+ raise NotImplementedError
+
+ def __call__(self, char * buffer, int length):
+ return self.parse( buffer, length )
cdef class asTuple(Parser):
'''converts a :term:`tabix row` into a python tuple.
Access is by numeric index.
'''
- def __call__(self, char * buffer, int len):
+ cdef parse(self, char * buffer, int len):
cdef TabProxies.TupleProxy r
r = TabProxies.TupleProxy()
# need to copy - there were some
@@ -422,7 +441,7 @@ cdef class asGTF(Parser):
the transcript identifier
'''
- def __call__(self, char * buffer, int len):
+ cdef parse(self, char * buffer, int len):
cdef TabProxies.GTFProxy r
r = TabProxies.GTFProxy()
r.copy( buffer, len )
@@ -462,7 +481,7 @@ cdef class asBed( Parser ):
need to be defined as well.
'''
- def __call__(self, char * buffer, int len):
+ cdef parse(self, char * buffer, int len):
cdef TabProxies.BedProxy r
r = TabProxies.BedProxy()
r.copy( buffer, len )
@@ -498,7 +517,7 @@ cdef class asVCF( Parser ):
second_sample_genotype = vcf[1]
'''
- def __call__(self, char * buffer, int len ):
+ cdef parse(self, char * buffer, int len ):
cdef TabProxies.VCFProxy r
r = TabProxies.VCFProxy()
r.copy( buffer, len )
@@ -552,10 +571,9 @@ cdef class TabixIteratorParsed:
while 1:
s = ti_read(self.tabixfile, self.iterator, &len)
if s == NULL: raise StopIteration
- # todo: read metachar from configuration
if s[0] != '#': break
- return self.parser(s, len)
+ return self.parser.parse(s, len)
def __dealloc__(self):
if <void*>self.iterator != NULL:
@@ -670,7 +688,7 @@ def tabix_index( filename,
'gff' : ( 0, 1, 4, 5, ord('#'), 0 ),
'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ),
'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ),
- 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ),
+ 'sam' : ( 1, 3, 4, 0, ord('@'), 0 ),
'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ),
'pileup': (3, 1, 2, 0, ord('#'), 0 ),
}
@@ -701,88 +719,119 @@ def tabix_index( filename,
return filename
-#########################################################
-#########################################################
-#########################################################
-## Iterators for parsing through unindexed files.
-#########################################################
-ctypedef class tabix_inplace_iterator:
- '''iterate over ``infile``.
+# #########################################################
+# #########################################################
+# #########################################################
+# ## Iterators for parsing through unindexed files.
+# #########################################################
+# cdef class tabix_file_iterator_old:
+# '''iterate over ``infile``.
- This iterator is not safe. If the :meth:`__next__()` method is called
- after ``infile`` is closed, the result is undefined (see ``fclose()``).
+# This iterator is not safe. If the :meth:`__next__()` method is called
+# after ``infile`` is closed, the result is undefined (see ``fclose()``).
- The iterator might either raise a StopIteration or segfault.
- '''
+# The iterator might either raise a StopIteration or segfault.
+# '''
- def __cinit__(self, infile, int buffer_size = 65536 ):
+# def __cinit__(self,
+# infile,
+# Parser parser,
+# int buffer_size = 65536 ):
- cdef int fd = PyObject_AsFileDescriptor( infile )
- if fd == -1: raise ValueError( "I/O operation on closed file." )
- self.infile = fdopen( fd, 'r')
+# cdef int fd = PyObject_AsFileDescriptor( infile )
+# if fd == -1: raise ValueError( "I/O operation on closed file." )
+# self.infile = fdopen( fd, 'r')
- if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
+# if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
- self.buffer = <char*>malloc( buffer_size )
- self.size = buffer_size
+# self.buffer = <char*>malloc( buffer_size )
+# self.size = buffer_size
+# self.parser = parser
- def __iter__(self):
- return self
+# def __iter__(self):
+# return self
- cdef __cnext__(self):
+# cdef __cnext__(self):
- cdef char * b
- cdef size_t nbytes
- b = self.buffer
- r = self.Parser()
+# cdef char * b
+# cdef size_t nbytes
+# b = self.buffer
- while not feof( self.infile ):
- nbytes = getline( &b, &self.size, self.infile)
+# while not feof( self.infile ):
+# nbytes = getline( &b, &self.size, self.infile)
- # stop at first error or eof
- if (nbytes == -1): break
- # skip comments
- if (b[0] == '#'): continue
+# # stop at first error or eof
+# if (nbytes == -1): break
+# # skip comments
+# if (b[0] == '#'): continue
- # skip empty lines
- if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue
+# # skip empty lines
+# if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue
- # make sure that entry is complete
- if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
- result = b
- raise ValueError( "incomplete line at %s" % result )
+# # make sure that entry is complete
+# if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
+# result = b
+# raise ValueError( "incomplete line at %s" % result )
- # make sure that this goes fully through C
- # otherwise buffer is copied to/from a
- # Python object causing segfaults as
- # the wrong memory is freed
- r.present( b, nbytes )
- return r
+# # make sure that this goes fully through C
+# # otherwise buffer is copied to/from a
+# # Python object causing segfaults as
+# # the wrong memory is freed
+# return self.parser.parse( b, nbytes )
- raise StopIteration
+# raise StopIteration
- def __dealloc__(self):
- free(self.buffer)
+# def __dealloc__(self):
+# free(self.buffer)
- def __next__(self):
- return self.__cnext__()
+# def __next__(self):
+# return self.__cnext__()
-ctypedef class tabix_copy_iterator:
- '''iterate over ``infile``.
+#########################################################
+#########################################################
+#########################################################
+## Iterators for parsing through unindexed files.
+#########################################################
+cdef buildGzipError(void *gzfp):
+ cdef int errnum = 0
+ cdef const char *s = gzerror(gzfp, &errnum)
+ return "error (%d): %s (%d: %s)" % (errno, strerror(errno), errnum, s)
- This iterator is not save. If the :meth:`__next__()` method is called
- after ``infile`` is closed, the result is undefined (see ``fclose()``).
- The iterator might either raise a StopIteration or segfault.
+cdef class tabix_file_iterator:
+ '''iterate over a compressed or uncompressed ``infile``.
'''
- def __cinit__(self, infile, Parser parser ):
+ def __cinit__(self,
+ infile,
+ Parser parser,
+ int buffer_size = 65536 ):
+
+ if infile.closed:
+ raise ValueError( "I/O operation on closed file." )
+
+ self.infile = infile
cdef int fd = PyObject_AsFileDescriptor( infile )
if fd == -1: raise ValueError( "I/O operation on closed file." )
- self.infile = fdopen( fd, 'r')
- if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
+
+ # From the manual:
+ # gzopen can be used to read a file which is not in gzip format;
+ # in this case gzread will directly read from the file without decompression.
+ # When reading, this will be detected automatically by looking
+ # for the magic two-byte gzip header.
+ self.fh = gzdopen( fd, 'r')
+
+ if self.fh == NULL:
+ raise IOError('%s' % strerror(errno))
+
+ self.ks = ks_init( self.fh)
+
+ self.buffer.s = <char*>malloc( buffer_size )
+ #if self.buffer == NULL:
+ # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size)
+ #self.size = buffer_size
self.parser = parser
def __iter__(self):
@@ -791,42 +840,39 @@ ctypedef class tabix_copy_iterator:
cdef __cnext__(self):
cdef char * b
- cdef size_t nbytes
- cdef int x
-
- b = NULL
-
- while not feof( self.infile ):
+ cdef int dret = 0
+ cdef int retval = 0
+ while 1:
+
+ retval = ks_getuntil(self.ks, '\n', &self.buffer, &dret)
+
+ if retval < 0:
+ break
+ #raise IOError('gzip error: %s' % buildGzipError( self.fh ))
- # getline allocates on demand
- # return number of characters read excluding null byte
- nbytes = getline( &b, &nbytes, self.infile)
- # stop at first error
- if (nbytes == -1): break
+ b = self.buffer.s
+
# skip comments
if (b[0] == '#'): continue
# skip empty lines
if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue
- # make sure that entry is complete
- if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
- result = b
- free(b)
- raise ValueError( "incomplete line at %s" % result )
-
- # make sure that this goes fully through C
- # otherwise buffer is copied to/from a
- # Python object causing segfaults as
- # the wrong memory is freed
- # -1 to remove the new-line character
- return self.parser(b, nbytes)
-
- free(b)
+ # gzgets terminates at \n, no need to test
+
+ # parser creates a copy
+ return self.parser.parse( b, self.buffer.l )
+
raise StopIteration
+ def __dealloc__(self):
+ free(self.buffer.s)
+
def __next__(self):
return self.__cnext__()
+
+ def next(self):
+ return self.__cnext__()
class tabix_generic_iterator:
'''iterate over ``infile``.
@@ -847,6 +893,11 @@ class tabix_generic_iterator:
cdef char * b, * cpy
cdef size_t nbytes
+
+ # note that GzipFile.close() does not close the file
+ # reading is still possible.
+ if self.infile.closed: raise ValueError( "I/O operation on closed file." )
+
while 1:
line = self.infile.readline()
@@ -879,10 +930,14 @@ class tabix_generic_iterator:
# python version - required for python 2.7
def next(self):
return self.__next__()
-
+
def tabix_iterator( infile, parser ):
"""return an iterator over all entries in a file."""
- return tabix_generic_iterator( infile, parser )
+ if PYTHON3:
+ return tabix_generic_iterator( infile, parser )
+ else:
+ return tabix_file_iterator( infile, parser )
+
# file objects can use C stdio
# used to be: isinstance( infile, file):
# if PYTHON3:
@@ -904,5 +959,6 @@ __all__ = ["tabix_index",
"asVCF",
"asBed",
"tabix_iterator",
- "tabix_inplace_iterator"
+ "tabix_generic_iterator",
+ "tabix_file_iterator",
]
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index 51f2cf0..dcb83b4 100644
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
+/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -260,6 +260,7 @@
#include "sys/stat.h"
#include "fcntl.h"
#include "unistd.h"
+#include "zlib.h"
#include "bgzf.h"
#include "tabix.h"
#include "tabix_util.h"
@@ -345,27 +346,26 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_6ctabix_Parser;
-struct __pyx_obj_5pysam_6ctabix_asBed;
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse;
+struct __pyx_obj_5pysam_6ctabix_Parser;
struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
struct __pyx_obj_5pysam_4cvcf_VCFRecord;
-struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data;
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
+struct __pyx_obj_5pysam_6ctabix_asBed;
+struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
struct __pyx_obj_5pysam_6ctabix_Tabixfile;
-struct __pyx_obj_5pysam_6ctabix_TabixIterator;
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
struct __pyx_obj_5pysam_10TabProxies_BedProxy;
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
-struct __pyx_obj_5pysam_6ctabix_asTuple;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
struct __pyx_defaults;
typedef struct __pyx_defaults __pyx_defaults;
struct __pyx_defaults1;
@@ -393,45 +393,6 @@ struct __pyx_defaults4 {
PyObject *__pyx_arg_lineparse;
};
-/* "ctabix.pxd":190
- * cdef tabix_t * tabixfile
- *
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_Parser {
- PyObject_HEAD
-};
-
-
-/* "ctabix.pxd":199
- * pass
- *
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asBed {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "ctabix.pxd":205
- * pass
- *
- * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
- */
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
- PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
-};
-
-
/* "pysam/cvcf.pyx":902
* return line
*
@@ -451,6 +412,19 @@ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse {
};
+/* "ctabix.pxd":232
+ * cdef tabix_t * tabixfile
+ *
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * cdef parse( self, char * buffer, int len )
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_Parser {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtab;
+};
+
+
/* "TabProxies.pxd":41
* ctypedef int uint64_t
*
@@ -471,72 +445,91 @@ struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
};
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
+/* "pysam/cvcf.pyx":95
+ * ###########################################################################################################
*
- * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
- * pass
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
*
*/
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+struct __pyx_obj_5pysam_4cvcf_VCFRecord {
struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ PyObject *vcf;
+ char *contig;
+ uint32_t pos;
};
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
+/* "ctabix.pxd":239
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
- * cdef:
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
*/
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_6ctabix_asGTF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "pysam/cvcf.pyx":95
- * ###########################################################################################################
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_obj_5pysam_4cvcf_VCFRecord {
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- PyObject *vcf;
- char *contig;
- uint32_t pos;
+ char *_attributes;
+ int hasOwnAttributes;
};
-/* "pysam/cvcf.pyx":229
+/* "ctabix.pxd":235
+ * cdef parse( self, char * buffer, int len )
*
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * cdef parse( self, char * buffer, int len )
*
- * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a VCF record.'''
- * cdef vcffile
*/
-struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
+struct __pyx_obj_5pysam_6ctabix_asTuple {
struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
- PyObject *vcffile;
};
-/* "ctabix.pxd":202
+/* "ctabix.pxd":242
* pass
*
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_asVCF {
+struct __pyx_obj_5pysam_6ctabix_asBed {
struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
+/* "ctabix.pxd":201
+ * int ks_getuntil( kstream_t *, int, kstring_t *, int * )
+ *
+ * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
+ * cdef gzFile fh
+ * cdef kstream_t * ks
+ */
+struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtab;
+ gzFile fh;
+ kstream_t *ks;
+ kstring_t buffer;
+ size_t size;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+ int fd;
+ PyObject *infile;
+};
+
+
/* "pysam/cvcf.pyx":650
* return False
*
@@ -550,72 +543,75 @@ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data {
};
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
+/* "pysam/cvcf.pyx":229
*
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
- * cdef:
+ * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a VCF record.'''
+ * cdef vcffile
*/
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+ PyObject *vcffile;
};
-/* "ctabix.pxd":186
- * cdef tabix_t * tabixfile
+/* "ctabix.pxd":212
+ * cdef __cnext__(self)
*
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ *
+ * # pointer to tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
PyObject_HEAD
- ti_iter_t iterator;
tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "ctabix.pxd":196
- * pass
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( self )
*
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_asGTF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
};
-/* "ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+/* "TabProxies.pxd":72
+ * pass
*
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
- * # pointer to tabixfile
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_Tabixfile {
- PyObject_HEAD
- tabix_t *tabixfile;
- int isremote;
- char *_filename;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
};
-/* "ctabix.pxd":182
- * cdef char * _filename
+/* "ctabix.pxd":248
+ * pass
*
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
* cdef ti_iter_t iterator
* cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
PyObject_HEAD
ti_iter_t iterator;
tabix_t *tabixfile;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
@@ -636,63 +632,57 @@ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr {
};
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "ctabix.pxd":245
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
- FILE *infile;
- char *buffer;
- size_t size;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_6ctabix_asVCF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":72
- * pass
- *
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+/* "ctabix.pxd":224
+ * cdef Parser parser
*
- * cdef:
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_10TabProxies_BedProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "ctabix.pxd":228
+ * cdef tabix_t * tabixfile
*
- * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "ctabix.pxd":193
- * pass
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_asTuple {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
};
@@ -715,6 +705,20 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
+/* "pysam/cvcf.pyx":95
+ * ###########################################################################################################
+ *
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
+
+
/* "TabProxies.pxd":69
* cdef char * getAttributes( self )
*
@@ -743,32 +747,60 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-/* "pysam/cvcf.pyx":95
- * ###########################################################################################################
+/* "ctabix.pxd":232
+ * cdef tabix_t * tabixfile
*
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * cdef parse( self, char * buffer, int len )
*
*/
-struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_6ctabix_Parser {
+ PyObject *(*parse)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int);
};
-static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
+static struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtabptr_5pysam_6ctabix_Parser;
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "ctabix.pxd":242
+ * pass
+ *
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
*/
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
+struct __pyx_vtabstruct_5pysam_6ctabix_asBed {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_asBed *__pyx_vtabptr_5pysam_6ctabix_asBed;
+
+
+/* "ctabix.pxd":201
+ * int ks_getuntil( kstream_t *, int, kstring_t *, int * )
+ *
+ * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
+ * cdef gzFile fh
+ * cdef kstream_t * ks
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *);
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator;
+
+
+/* "ctabix.pxd":245
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_asVCF {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asVCF *__pyx_vtabptr_5pysam_6ctabix_asVCF;
/* "TabProxies.pxd":72
@@ -785,18 +817,32 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "pysam/cvcf.pyx":229
*
- * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
+ *
+ * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a VCF record.'''
+ * cdef vcffile
*/
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *);
+struct __pyx_vtabstruct_5pysam_4cvcf_asVCFRecord {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
+static struct __pyx_vtabstruct_5pysam_4cvcf_asVCFRecord *__pyx_vtabptr_5pysam_4cvcf_asVCFRecord;
+
+
+/* "ctabix.pxd":239
+ *
+ *
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_asGTF {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asGTF *__pyx_vtabptr_5pysam_6ctabix_asGTF;
/* "TabProxies.pxd":60
@@ -812,6 +858,20 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
+
+
+/* "ctabix.pxd":235
+ * cdef parse( self, char * buffer, int len )
+ *
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * cdef parse( self, char * buffer, int len )
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_asTuple {
+ struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_asTuple *__pyx_vtabptr_5pysam_6ctabix_asTuple;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -1305,6 +1365,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'pysam.ctabix' */
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_file_iterator = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0;
@@ -1314,8 +1375,6 @@ static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0;
/* Module declarations from 'pysam.TabProxies' */
static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0;
@@ -23555,12 +23614,14 @@ static PyTypeObject __pyx_type_5pysam_4cvcf_VCFRecord = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_4cvcf_asVCFRecord __pyx_vtable_5pysam_4cvcf_asVCFRecord;
static PyObject *__pyx_tp_new_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p;
PyObject *o = __pyx_ptype_5pysam_6ctabix_Parser->tp_new(t, a, k);
if (!o) return 0;
p = ((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_4cvcf_asVCFRecord;
p->vcffile = Py_None; Py_INCREF(Py_None);
return o;
}
@@ -26080,8 +26141,12 @@ PyMODINIT_FUNC PyInit_cvcf(void)
if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf_VCFRecord = &__pyx_type_5pysam_4cvcf_VCFRecord;
__pyx_ptype_5pysam_6ctabix_Parser = __Pyx_ImportType("pysam.ctabix", "Parser", sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_Parser = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_Parser->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_4cvcf_asVCFRecord = &__pyx_vtable_5pysam_4cvcf_asVCFRecord;
+ __pyx_vtable_5pysam_4cvcf_asVCFRecord.__pyx_base = *__pyx_vtabptr_5pysam_6ctabix_Parser;
__pyx_type_5pysam_4cvcf_asVCFRecord.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
if (PyType_Ready(&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_4cvcf_asVCFRecord.tp_dict, __pyx_vtabptr_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf_asVCFRecord = &__pyx_type_5pysam_4cvcf_asVCFRecord;
if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -26091,18 +26156,20 @@ PyMODINIT_FUNC PyInit_cvcf(void)
if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse;
/*--- Type import code ---*/
- __pyx_ptype_5pysam_6ctabix_Tabixfile = __Pyx_ImportType("pysam.ctabix", "Tabixfile", sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_TabixIterator = __Pyx_ImportType("pysam.ctabix", "TabixIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = __Pyx_ImportType("pysam.ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_asTuple = __Pyx_ImportType("pysam.ctabix", "asTuple", sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_asGTF = __Pyx_ImportType("pysam.ctabix", "asGTF", sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_asBed = __Pyx_ImportType("pysam.ctabix", "asBed", sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_asVCF = __Pyx_ImportType("pysam.ctabix", "asVCF", sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = __Pyx_ImportType("pysam.ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_inplace_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_copy_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_tabix_file_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_file_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_file_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_file_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_Tabixfile = __Pyx_ImportType("pysam.ctabix", "Tabixfile", sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixIterator = __Pyx_ImportType("pysam.ctabix", "TabixIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = __Pyx_ImportType("pysam.ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asTuple = __Pyx_ImportType("pysam.ctabix", "asTuple", sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_asTuple = (struct __pyx_vtabstruct_5pysam_6ctabix_asTuple*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_asTuple->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asGTF = __Pyx_ImportType("pysam.ctabix", "asGTF", sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_asGTF = (struct __pyx_vtabstruct_5pysam_6ctabix_asGTF*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_asGTF->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asBed = __Pyx_ImportType("pysam.ctabix", "asBed", sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_asBed = (struct __pyx_vtabstruct_5pysam_6ctabix_asBed*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_asBed->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asVCF = __Pyx_ImportType("pysam.ctabix", "asVCF", sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_asVCF = (struct __pyx_vtabstruct_5pysam_6ctabix_asVCF*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_asVCF->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = __Pyx_ImportType("pysam.ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_10TabProxies_GTFProxy = __Pyx_ImportType("pysam.TabProxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_5pysam_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = __Pyx_ImportType("pysam.TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
diff --git a/pysam/tabix_util.c b/pysam/tabix_util.c
index 0305de1..89ffc23 100644
--- a/pysam/tabix_util.c
+++ b/pysam/tabix_util.c
@@ -1,5 +1,6 @@
// Definition of pysamerr
#include "stdio.h"
+#include "unistd.h"
FILE * pysamerr = NULL;
#if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700)
@@ -24,3 +25,4 @@ getline(char **line, size_t *linelen, FILE *fp)
}
#endif
+
diff --git a/pysam/tabix_util.h b/pysam/tabix_util.h
index 6a7db92..e3e38d1 100644
--- a/pysam/tabix_util.h
+++ b/pysam/tabix_util.h
@@ -1,6 +1,13 @@
/* See issue 122
On some MACOSX systems getline is not defined.
*/
+#include <zlib.h>
+#include "kseq.h"
+
#if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700)
+#include "unistd.h"
ssize_t getline(char **line, size_t *linelen, FILE *fp);
#endif
+
+KSTREAM_INIT( gzFile, gzread, 16384)
+
diff --git a/pysam/version.py b/pysam/version.py
index 0dfb2cf..c3375ad 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,6 +1,6 @@
# pysam versioning information
-__version__ = "0.7.6"
+__version__ = "0.7.7"
__samtools_version__ = "0.1.19"
diff --git a/tests/Makefile b/tests/Makefile
index 05963e5..e985e61 100644
--- a/tests/Makefile
+++ b/tests/Makefile
@@ -13,6 +13,7 @@ all: ex1.pileup.gz ex1.bam.bai \
example_user_header.bam \
example_btag.bam \
example_bai.bam \
+ softclip.bam
ex2.sam.gz: ex1.bam ex1.bam.bai
samtools view -h ex1.bam | gzip > ex2.sam.gz
@@ -42,8 +43,8 @@ example_bai.bam: ex1.bam
samtools index $@
mv $@.bai example_bai.bai
-
-
+softclip.bam: softclip.sam
+ samtools view -bS $< > $@
clean:
rm -fr *.bam *.bai *.fai *.pileup* \
diff --git a/tests/pysam_test.py b/tests/pysam_test.py
index 67f205f..3cb49bd 100755
--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -667,6 +667,40 @@ class TestTagParsing( unittest.TestCase ):
self.assertEqual( tags, r.tags )
+class TestClipping(unittest.TestCase):
+
+ def testClipping( self ):
+
+ self.samfile = pysam.Samfile("softclip.bam", "rb" )
+ for read in self.samfile:
+
+ if read.qname == "r001":
+ self.assertEqual( read.seq, b'AAAAGATAAGGATA' )
+ self.assertEqual( read.query, b'AGATAAGGATA' )
+ self.assertEqual( read.qual, None )
+ self.assertEqual( read.qqual, None )
+
+ elif read.qname == "r002":
+
+ self.assertEqual( read.seq, b'GCCTAAGCTAA' )
+ self.assertEqual( read.query, b'AGCTAA' )
+ self.assertEqual( read.qual, b'01234567890' )
+ self.assertEqual( read.qqual, b'567890' )
+
+ elif read.qname == "r003":
+
+ self.assertEqual( read.seq, b'GCCTAAGCTAA' )
+ self.assertEqual( read.query, b'GCCTAA' )
+ self.assertEqual( read.qual, b'01234567890' )
+ self.assertEqual( read.qqual, b'012345' )
+
+ elif read.qname == "r004":
+
+ self.assertEqual( read.seq, b'TAGGC' )
+ self.assertEqual( read.query, b'TAGGC' )
+ self.assertEqual( read.qual, b'01234' )
+ self.assertEqual( read.qqual, b'01234' )
+
class TestIteratorRow(unittest.TestCase):
def setUp(self):
@@ -980,7 +1014,24 @@ class TestHeaderBam(TestHeaderSam):
def setUp(self):
self.samfile=pysam.Samfile( "ex3.bam","rb" )
+class TestHeaderFromRefs( unittest.TestCase ):
+ '''see issue 144
+
+ reference names need to be converted to string for python 3
+ '''
+ def testHeader( self ):
+ refs = ['chr1', 'chr2']
+ tmpfile = "tmp_%i" % id(self)
+ s = pysam.Samfile(tmpfile, 'wb',
+ referencenames=refs,
+ referencelengths=[100]*len(refs))
+ s.close()
+
+ self.assertTrue( checkBinaryEqual( 'issue144.bam', tmpfile ),
+ 'bam files differ')
+ os.unlink( tmpfile )
+
class TestHeader1000Genomes( unittest.TestCase ):
# bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam"
@@ -1150,6 +1201,7 @@ class TestFastaFile(unittest.TestCase):
# unknown sequence returns ""
+ # change: should be an IndexError
self.assertEqual( b"", self.file.fetch("chr12") )
def testOutOfRangeAccess( self ):
@@ -1162,12 +1214,19 @@ class TestFastaFile(unittest.TestCase):
def testFetchErrors( self ):
self.assertRaises( ValueError, self.file.fetch )
- self.assertRaises( ValueError, self.file.fetch, "chr1", -1, 10 )
+ self.assertRaises( IndexError, self.file.fetch, "chr1", -1, 10 )
self.assertRaises( ValueError, self.file.fetch, "chr1", 20, 10 )
+
+ # does not work yet
+ # self.assertRaises( KeyError, self.file.fetch, "chrX" )
def testLength( self ):
self.assertEqual( len(self.file), 2 )
+ def testSequenceLengths( self ):
+ self.assertEqual( 1575, self.file.getReferenceLength( "chr1" ) )
+ self.assertEqual( 1584, self.file.getReferenceLength( "chr2" ) )
+
def tearDown(self):
self.file.close()
diff --git a/tests/tabix_test.py b/tests/tabix_test.py
index 3477340..90c2340 100644
--- a/tests/tabix_test.py
+++ b/tests/tabix_test.py
@@ -28,22 +28,32 @@ def myzip_open( infile, mode = "r" ):
else:
return gzip.open( mode )
-def loadAndConvert( infile ):
- '''load and convert all fields to bytes'''
+def loadAndConvert( infile, encode = True ):
+ '''load data from infile and convert all fields to bytes.
+
+ infile can be either plain or compressed (ending in .gz).
+ '''
data = []
if infile.endswith(".gz"):
for line in gzip.open( infile ):
line = line.decode("ascii")
if line.startswith("#"): continue
d = line.strip().split("\t")
- data.append( [x.encode("ascii") for x in d ] )
+ if encode:
+ data.append( [x.encode("ascii") for x in d ] )
+ else:
+ data.append( d )
+
else:
with open(infile) as f:
for line in f:
if line.startswith("#"): continue
d = line.strip().split("\t")
- data.append( [x.encode("ascii") for x in d ] )
-
+ if encode:
+ data.append( [x.encode("ascii") for x in d ] )
+ else:
+ data.append( d )
+
return data
def splitToBytes( s ):
@@ -91,32 +101,62 @@ class TestIndexing(unittest.TestCase):
class TestCompression(unittest.TestCase):
filename = "example.gtf.gz"
filename_idx = "example.gtf.gz.tbi"
+ preset = "gff"
def setUp( self ):
- self.tmpfilename = "tmp_%i.gtf" % id(self)
+ self.tmpfilename = "tmp_%i" % id(self)
infile = gzip.open( self.filename, "rb")
outfile = open( self.tmpfilename, "wb" )
outfile.write( infile.read() )
outfile.close()
infile.close()
- def testIndexPreset( self ):
+ def testCompression( self ):
+ '''see also issue 106'''
+ pysam.tabix_compress( self.tmpfilename, self.tmpfilename + ".gz" )
+ checkBinaryEqual( self.tmpfilename, self.tmpfilename + ".gz" )
+
+ def testIndexPresetUncompressed( self ):
'''test indexing via preset.'''
- pysam.tabix_index( self.tmpfilename, preset = "gff" )
+ pysam.tabix_index( self.tmpfilename, preset = self.preset )
+ # check if uncompressed file has been removed
+ self.assertEqual( os.path.exists( self.tmpfilename ), False )
checkBinaryEqual( self.tmpfilename + ".gz", self.filename )
checkBinaryEqual( self.tmpfilename + ".gz.tbi", self.filename_idx )
- def testCompression( self ):
- '''see also issue 106'''
+ def testIndexPresetCompressed( self ):
+ '''test indexing via preset.'''
+
pysam.tabix_compress( self.tmpfilename, self.tmpfilename + ".gz" )
- checkBinaryEqual( self.tmpfilename, self.tmpfilename + ".gz" )
+ pysam.tabix_index( self.tmpfilename + ".gz", preset = self.preset )
+ checkBinaryEqual( self.tmpfilename + ".gz", self.filename )
+ checkBinaryEqual( self.tmpfilename + ".gz.tbi", self.filename_idx )
def tearDown( self ):
- os.unlink( self.tmpfilename + ".gz" )
- if os.path.exists( self.tmpfilename + ".gz.tbi" ):
+
+ try:
+ os.unlink( self.tmpfilename )
+ os.unlink( self.tmpfilename + ".gz" )
os.unlink( self.tmpfilename + ".gz.tbi" )
+ except OSError:
+ pass
+
+class TestCompressionSam( TestCompression ):
+ filename = "example.sam.gz"
+ filename_index = "example.sam.gz.tbi"
+ preset = "sam"
+
+class TestCompressionBed( TestCompression ):
+ filename = "example.bed.gz"
+ filename_index = "example.bed.gz.tbi"
+ preset = "bed"
+
+class TestCompressionVCF( TestCompression ):
+ filename = "example.vcf.gz"
+ filename_index = "example.vcf.gz.tbi"
+ preset = "vcf"
class TestIteration( unittest.TestCase ):
@@ -231,11 +271,23 @@ class TestIteration( unittest.TestCase ):
def testInvalidIntervals( self ):
+ # invalid intervals (start > end)
self.assertRaises( ValueError, self.tabix.fetch, "chr1", 0, -10)
- self.assertRaises( ValueError, self.tabix.fetch, "chr1", -10, 200)
self.assertRaises( ValueError, self.tabix.fetch, "chr1", 200, 0)
- self.assertRaises( ValueError, self.tabix.fetch, "chr1", -10, -20)
- self.assertRaises( ValueError, self.tabix.fetch, "chrUn" )
+
+ # out of range intervals
+ self.assertRaises( IndexError, self.tabix.fetch, "chr1", -10, 200)
+ self.assertRaises( IndexError, self.tabix.fetch, "chr1", -10, -20)
+
+ # unknown chromosome
+ self.assertRaises( KeyError, self.tabix.fetch, "chrUn" )
+
+ # out of range access
+ # to be implemented
+ # self.assertRaises( IndexError, self.tabix.fetch, "chr1", 1000000, 2000000 )
+
+ # raise no error for invalid intervals
+ self.tabix.fetch( "chr1", 100,100)
def testGetContigs( self ):
self.assertEqual( sorted(self.tabix.contigs), [b"chr1", b"chr2"] )
@@ -360,6 +412,85 @@ class TestParser( unittest.TestCase ):
os.unlink( tmpfilename )
+class TestIterators( unittest.TestCase ):
+
+ filename = "example.gtf.gz"
+
+ iterator = pysam.tabix_generic_iterator
+ parser = pysam.asTuple
+ is_compressed = False
+
+ def setUp( self ):
+
+ self.tabix = pysam.Tabixfile( self.filename )
+ self.compare = loadAndConvert( self.filename )
+ self.tmpfilename_uncompressed = 'tmp_TestIterators'
+ infile = gzip.open( self.filename, "rb")
+ outfile = open( self.tmpfilename_uncompressed, "wb" )
+ outfile.write( infile.read() )
+ outfile.close()
+ infile.close()
+
+ def open( self ):
+
+ if self.is_compressed:
+ infile = gzip.open( self.filename )
+ else:
+ infile = open( self.tmpfilename_uncompressed )
+ return infile
+
+ def testIteration( self ):
+
+ infile = self.open()
+
+ for x, r in enumerate(self.iterator( infile, self.parser())):
+ self.assertEqual( self.compare[x], list(r) )
+ self.assertEqual( len(self.compare[x]), len(r) )
+
+ # test indexing
+ for c in range(0,len(r)):
+ self.assertEqual( self.compare[x][c], r[c] )
+
+ # test slicing access
+ for c in range(0, len(r)-1):
+ for cc in range(c+1, len(r)):
+ self.assertEqual( self.compare[x][c:cc],
+ r[c:cc] )
+
+ def testClosedFile( self ):
+ '''test for error when iterating from closed file.'''
+ infile = self.open()
+ infile.close()
+
+ # iterating from a closed file should raise a value error
+ self.assertRaises( ValueError, self.iterator, infile, self.parser())
+
+ def testClosedFileIteration( self ):
+ '''test for error when iterating from file that has been closed'''
+
+ infile = self.open()
+
+ i = self.iterator( infile, self.parser())
+ x = i.next()
+ infile.close()
+ # Not implemented
+ #self.assertRaises( ValueError, i.next )
+
+ def tearUp( self ):
+ os.unlink( self.tmpfilename_uncompressed )
+
+class TestIteratorsGenericCompressed( TestIterators ):
+ is_compressed = True
+
+class TestIteratorsFileCompressed( TestIterators ):
+ iterator = pysam.tabix_file_iterator
+ is_compressed = True
+
+class TestIteratorsFileUncompressed( TestIterators ):
+ iterator = pysam.tabix_file_iterator
+ is_compressed = False
+
+
class TestGTF( TestParser ):
def testRead( self ):
@@ -527,7 +658,7 @@ class TestVCFFromVCF( TestVCF ):
TestVCF.setUp( self )
self.vcf = pysam.VCF()
- self.compare = loadAndConvert( self.filename )
+ self.compare = loadAndConvert( self.filename, encode = False )
def testParsing( self ):
@@ -612,7 +743,7 @@ class TestVCFFromVCF( TestVCF ):
else:
self.assertEqual( c[y], val,
"mismatch in field %s: expected %s, got %s" %\
- ( field,c[y], val ) )
+ ( field, c[y], val ) )
############################################################################
# create a test class for each example vcf file.
--
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